Convergent Evolution

The common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse "true spiders" (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of multiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of true spiders. This robust phylogenomic framework was used to conduct maximum likelihood and Bayesian character evolution analyses for respiratory systems, silk glands, and aerial webs, based on a combination of original and published data. Our results indicate that in true spiders, posterior book lungs were transformed into morphologically similar tracheal systems six times independently, after the evolution of novel silk gland systems and the origin of aerial webs. From these comparative data, we put forth a novel hypothesis that early-diverging web-building spiders were faced with new energetic demands for spinning, which prompted the evolution of similar tracheal systems via convergence; we also propose tests of predictions derived from this hypothesis.[Book lungs; discrete character evolution; respiratory systems; silk; spider web evolution; ultraconserved elements.]

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of l...

Marine tetrapod clades (e.g. seals, whales) independently adapted to marine life through the Mesozoic and Caenozoic, and provide iconic examples of convergent evolution. Apparent morphological convergence is often explained as the result of adaptation to similar ecological niches. However, quantitative tests of this hypothesis are uncommon. We use dietary data to classify the feeding ecology of extant marine tetrapods and identify patterns in skull and tooth morphology that discriminate trophic groups across clades. Mapping these patterns onto phylogeny reveals coordinated evolutionary shifts in diet and morphology in different marine tetrapod lineages. Similarities in morphology between species with similar diets—even across large phylogenetic distances—are consistent with previous hypotheses that shared functional constraints drive convergent evolution in marine tetrapods.

Numerical codes based on a direct implementation of the standard ADM formulation of Einstein's equations have generally failed to provide long-term stable and convergent evolutions of black hole spacetimes when excision is used to remove the singularities. We show that, for the case of a single black hole in spherical symmetry, it is possible to circumvent these problems by adding to the evolution equations terms involving the constraints, thus adjusting the standard ADM system. We investigate the effect that the choice of the lapse and shift has on the stability properties of numerical simulations and thus on the form of the added constraint term. To facilitate this task, we introduce the concept of quasi well-posedness, a version of well-posedness suitable for ADM-like systems involving second-order spatial derivatives.

Quantitative analyses based upon the superimposition of phylogenetic and reproductive data have revealed that viviparity has originated on at least 132 independent occasions among vertebrates, with 98 of these origins having occurred among reptiles. The viviparous lineages have given rise to at least 24 matrotrophic clades, all but four of which are anamniotes. Traditional scenarios assume progressive, gradualistic evolution from oviparity to lecithotrophic viviparity to matrotrophic viviparity. However, mammalian evidence indicates that matrotrophy can precede the evolution of viviparity. Moreover, data on reptiles seem to be consistent with a punctuated equilibrium model for viviparity and a saltatory model for incipient matrotrophy and placentation. Among the specializations for fetal nutrition, strong convergence is evident at organismal, organological, and cytological levels. Examples include yolk sac placentation, trophotaeniae, and adaptations for embryonic cannibalism. Certain lizards of the genera Mabuya and Chalcides have converged strongly on eutherian mammals with respect to morphology of the chorioallantoic placenta. Placental specializations that have evolved independently in some eutherians and matrotrophic lizards include placentomes, giant binucleate cells, deciduate maternal tissue, and chorionic areolae.

Simple Summary Hedgehogs, being insectivores with slow metabolisms, are quite sensitive to temperature and food availability. As a consequence, their ranges have oscillated in relation to past climate changes. Species that have evolved in different regions, but their ranges have shifted and overlapped subsequently, often represent intense competitors as a result of ecological similarities. The present study focuses on this phenomenon in the contact zone in central Europe and adjacent regions, using genetic determination of species and description of size and shape of skull, the morphological structure mirroring many selection pressures related to ecology. While animals living outside of the contact zone show marked differences between the two species, individuals within the contact zone are more alike with a smaller skull size and a convergent jawbone shape. Changes in skull size can be related to inter-species competition and also facilitated by selection pressure, mediated by over...

Feeding and oviposition deterrents help phytophagous insects to identify host plants. The taste organs of phytophagous insects contain bitter gustatory receptors (GRs). To explore their function, we focused on PxylGr34, a bitter GR in Plutella xylostella (L.). We detected abundant PxylGr34 transcripts in the larval head and specific expression of PxylGr34 in the antennae of females. Analyses using the Xenopus oocyte expression system and two-electrode voltage-clamp recording showed that PxylGr34 is specifically tuned to the plant hormone brassinolide (BL) and its analog 24epibrassinolide. Electrophysiological analyses revealed that the medial sensilla styloconica on the maxillary galea of the 4 th instar larvae are responsive to BL. Dualchoice bioassays demonstrated that BL inhibits larval feeding and female ovipositing. Knock-down of PxylGr34 by RNAi abolished BL-induced feeding inhibition. These results shed light on gustatory coding mechanisms and deterrence of insect feeding and ovipositing, and may be useful for designing plant hormone-based pest management strategies. .

The bryophytes comprise three phyla of embryophytes that are well established to occupy the first nodes among extant lineages in the land-plant tree of life. The three bryophyte groups (hornworts, liverworts, mosses) may not form a monophyletic clade, but they share life history features including dominant free-living gametophytes and matrotrophic monosporangiate sporophytes. Because of their unique vegetative and reproductive innovations and their critical position in embryophyte phylogeny, studies of bryophytes are crucial to understanding the evolution of land plant morphology and genomes. This review focuses on phylogenetic relationships within each of the three divisions of bryophytes and relates morphological diversity to new insights about those relationships. Most previous work has been on the mosses, but progress on understanding the phylogeny of hornworts and liverworts is advancing at a rapid pace. Multilocus multigenome studies have been successful at resolving deep relationships within the mosses and liverworts, whereas singlegene analyses have advanced understanding of hornwort evolution.

The bryophytes comprise three phyla of embryophytes that are well established to occupy the first nodes among extant lineages in the land-plant tree of life. The three bryophyte groups (hornworts, liverworts, mosses) may not form a monophyletic clade, but they share life history features including dominant free-living gametophytes and matrotrophic monosporangiate sporophytes. Because of their unique vegetative and reproductive innovations and their critical position in embryophyte phylogeny, studies of bryophytes are crucial to understanding the evolution of land plant morphology and genomes. This review focuses on phylogenetic relationships within each of the three divisions of bryophytes and relates morphological diversity to new insights about those relationships. Most previous work has been on the mosses, but progress on understanding the phylogeny of hornworts and liverworts is advancing at a rapid pace. Multilocus multigenome studies have been successful at resolving deep relationships within the mosses and liverworts, whereas singlegene analyses have advanced understanding of hornwort evolution.

Comparative analysis of the organization and expression patterns of divergent and convergent gene pairs in multiple plant genomes can identify patterns that are shared by more than one species or are unique to a particular species. Here, we study the coexpression and interspecies conservation of divergent and convergent gene pairs in three plant species: rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and black cottonwood (Populus trichocarpa). Strongly correlated expression levels between divergent and convergent genes were found to be quite common in all three species, and the frequency of strong correlation appears to be independent of intergenic distance. Conservation of divergent or convergent arrangement among these species appears to be quite rare. However, conserved arrangement is significantly more frequent when the genes display strongly correlated expression levels or have one or more Gene Ontology (GO) classes in common. A correlation between intergenic distance...

Comparative analysis of the organization and expression patterns of divergent and convergent gene pairs in multiple plant genomes can identify patterns that are shared by more than one species or are unique to a particular species. Here, we study the coexpression and interspecies conservation of divergent and convergent gene pairs in three plant species: rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and black cottonwood (Populus trichocarpa). Strongly correlated expression levels between divergent and convergent genes were found to be quite common in all three species, and the frequency of strong correlation appears to be independent of intergenic distance. Conservation of divergent or convergent arrangement among these species appears to be quite rare. However, conserved arrangement is significantly more frequent when the genes display strongly correlated expression levels or have one or more Gene Ontology (GO) classes in common. A correlation between intergenic distance...

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest struct...

Background: Kinorhynch segmentation differs from the patterns found in Chordata, Arthropoda and Annelida which have coeloms and circulatory systems. Due to these differences and their obsolete status as 'Aschelminthes' , the microscopic kinorhynchs are often not acknowledged as segmented bilaterians. Yet, morphological studies have shown a conserved segmental arrangement of ectodermal and mesodermal organ systems with spatial correspondence along the anterior-posterior axis. However, a few aberrant kinorhynch lineages present a worm-like body plan with thin cuticle and less distinct segmentation, and thus their study may aid to shed new light on the evolution of segmental patterns within Kinorhyncha. Results: Here we found the nervous system in the aberrant Cateria styx and Franciscideres kalenesos to be clearly segmental, and similar to those of non-aberrant kinorhynchs; hereby not mirroring their otherwise aberrant and posteriorly shifted myoanatomy. In Zelinkaderes yong, however, the segmental arrangement of the nervous system is also shifted posteriorly and misaligned with respect to the cuticular segmentation. The morphological disparity together with the distant phylogenetic positions of F. kalenesos, C. styx and Z. yong support a convergent origin of aberrant appearances and segmental mismatches within Kinorhyncha.

Across Annelida, accessing the water column drives morphological and lifestyle modifications-yet in the primarily "benthic" scale worms, the ecological significance of swimming has largely been ignored. We investigated genetic, morphological and behavioural adaptations associated with swimming across Polynoidae, using mitogenomics and comparative methods. Mitochondrial genomes from cave and pelagic polynoids were highly similar, with non-significant rearrangements only present in cave Gesiella. Gene orders of the new mitogenomes were highly similar to shallow water species, suggestive of an underlying polynoid ground pattern. Being the first phylogenetic analyses to include the holopelagic Drieschia, we recovered this species nested among shallow water terminals, suggesting a shallow water ancestry. Based on these results, our phylogenetic reconstructions showed that swimming evolved independently three times in Polynoidae, involving convergent adaptations in morphology and motility patterns across the deep sea (Branchipolynoe), midwater (Drieschia) and anchialine caves (Pelagomacellicephala and Gesiella). Phylogenetic generalized least-squares (PGLS) analyses showed that holopelagic and anchialine cave species exhibit hypertrophy of the dorsal cirri, yet, these morphological modifications are achieved along different evolutionary pathways, i.e., elongation of the cirrophore versus style. Together, these findings suggest that a water column lifestyle elicits similar morphological adaptations, favouring bodies designed for drifting and sensing. Pelagic annelids are largely understudied, with poorly known origins, an unrecognized diversity and delicate bodies. Their mystery lies in their original discovery, which in most cases, dates back several centuries and are based on single observations of often incomplete or damaged specimens 1 . Yet, annelids are not uncommon throughout the oceanic water column, the midwater, with several groups containing only holopelagic species, including Lopadorrhynchidae, Iospilidae, Typhloscolecidae, Tomopteridae 2 , Alciopini, and Ctenophoricola 3 . Among the obligate holopelagic groups, evolution has driven numerous morphological specializations, including well-developed eyes (Alciopini), transparent bodies (Tomopteridae), specialized feeding and reproductive modes (Lopadorrhynchidae, Ctenophoricola) and creative defensive strategies (Alciopini 4,5 ; Swima 6 ). Holopelagic species are found within several other annelid families too, and are assumed to have evolved by opportunistic colonization events within otherwise benthic lineages. Such examples include Poeobius and Flota, two unrelated holopelagic genera within the otherwise benthic Flabelligeridae 7 , Swima and Teuthidodrilus within Acrocirridae 8 , Alciopini and Ctenophoricola within Phyllodocidae 3 and Chaetopterus pugaporcinus Osborn, Rouse, Goffredi & Robison, 2007 within the tube dwelling Chaetopteridae 9 . Several other annelid representatives can be found in the water column, but distinguishing truly pelagic forms from late stage larvae, or species with periodic swimming has proven challenging given the limited amount of direct observations available. Countless records of "benthic" annelids being collected from the water column are known 2 , but much work remains before we understand the true significance of benthic-pelagic interactions in annelids. Holopelagic species described from otherwise benthic groups often exhibit morphological adaptations that are convergent with those seen in exclusively holopelagic clades 2 . Regardless of their origin, annelids using the water column as habitat have undergone shifts in their behaviour and posture, specifically with regards to motility and lifestyle 10 . Some holopelagic species appear to swim continuously (e.g., Alciopini), many alternating between active swimming and drifting (e.g., Tomopteridae, Swima, Poeobius, and Flota) and others only drifting as in Chaetopterus pugaporcinus.

Relationships among the historically isolated lineages of Pseudobarbus were reconstructed using molecular and morphological data. Contradictions between the molecular and morphological phylogenies suggest convergent evolution and homoplasy in some morphological characters. The earliest divergence in Pseudobarbus was between P. quathlambae in Lesotho and the rest of the genus associated with the Cape Foristic Region in South Africa. A close relationship between P. phlegethon from the Olifants River system on the west coast of South Africa and a lineage of P. afer from small river systems in Afrotemperate Forests on the south coast, can only be explained through previous occurrence and subsequent extinction of ancestral populations in the Gourits River system. Several river systems had confluences before reaching lower sea levels, most notably during the last glacial maximum about 18,000 years ago, explaining closely related populations across different river systems. Mainly river capture explains shared lineages across river systems that did not share a common confluence during lower sea levels.

Extracellular DNA traps (ETs) are evolutionarily conserved antimicrobial mechanisms present in protozoa, plants, and animals. In this review, we compare their similarities in species of different taxa, and put forward the hypothesis that ETs have multiple origins. Our results are consistent with a process of evolutionary convergence in multicellular organisms through the application of a congruency test. Furthermore, we discuss why multicellularity is related to the presence of a mechanism initiating the formation of ETs.

Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). 'Lithistida', a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of 'lithistid' demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into th...

The pinnipeds, which comprise seals, sea lions, and walruses, are a remarkable group of marine animals with unique adaptations to semi-aquatic life. However, their genomes are poorly characterized. In this study, we sequenced and characterized the genomes of three pinnipeds (Phoca largha, Callorhinus ursinus, and Eumetopias jubatus), focusing on site-wise sequence changes. We detected rapidly evolving genes in pinniped lineages and substitutions unique to pinnipeds associated with amphibious sound perception. Phenotypic convergence-related sequence convergences are not common in marine mammals. For example, FASN, KCNA5, and IL17RA contain substitutions specific to pinnipeds, yet are potential candidates of phenotypic convergence (blubber, response to hypoxia, and immunity to pathogens) in all marine mammals. The outcomes of this study will provide insight into targets for future studies of convergent evolution or gene function.

OmpA is an important constituent of the outer membrane of Gram-negative bacteria. OmpA is involved in a variety of host-bacteria interactions, including crossing of the blood-brain barrier by E. coli strains causing newborn meningitis, and elicits a significant response by the immune system of the host. The bactericidal effect of neutrophil elastase (NE) is also attributed to degradation of the bacterial OmpA. Here we examined the OmpA of septicemic E. coli O78 strains and show that two surface-exposed loops are conserved among invasive strains of E. coli and other pathogenic Enterobacteriaceae. In addition, there is evidence for convergent evolution, implying the existence of selective pressure. Our results also indicate that large quantities of OmpA are secreted into the medium during all phases of growth, where it is present both in secreted vesicles and as a soluble secreted protein. We assume that secreted OmpA can play a role in protection of bacteria from NE by competitive inhibition. Support for this assumption was obtained from experiments indicating that addition of exogenous, purified OmpA reduces killing of bacteria by NE.

Knowledge of avian phylogeny is prerequisite to understanding the circumstances and timing of the diversification of birds and the evolution of morphological, behavioral, and life-history traits. Recent molecular datasets have helped to elucidate the three most basal clades in the tree of living birds, but relationships among neoavian orders (the vast majority of birds) remain frustratingly vexing. Here, we examine intron 7 of the ␤-fibrinogen gene in the most taxonomically inclusive survey of DNA sequences of nonpasserine bird families and orders to date. These data suggest that Neoaves consist of two sister clades with ecological parallelisms comparable to those found between marsupial and placental mammals. Some members of the putative respective clades have long been recognized as examples of convergent evolution, but it was not appreciated that they might be parts of diverse parallel radiations. In contrast, some traditional orders of birds are suggested by these data to be polyphyletic, with representative families in both radiations.

Motivation: Protein interactions provide an important context for the understanding of function. Experimental approaches have been complemented with computational ones, such as PSIMAP, which computes domain–domain interactions for all multi-domain and multi-chain proteins in the Protein Data Bank (PDB). PSIMAP has been used to determine that superfamilies occurring in many species have many interaction partners, to show examples of convergent evolution through shared interaction partners and to uncover complexes in the interaction map. To determine an interaction, the original PSIMAP algorithm checks all residue pairs of any domain pair defined by classification systems such as SCOP. The computation takes several days for the PDB. The computation of PSIMAP has two shortcomings: first, the original PSIMAP algorithm considers only interactions of residue pairs rather than atom pairs losing information for detailed analysis of contact patterns. At the atomic level the original algorith...

Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here, we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two proteins that bind and transport juvenile hormone (JH) – a key regulator of insect development and reproduction. We find one of these JH binding proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behavior and suggest eusocial evolution was fa...

Background: Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance. Methods: To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. Results: The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites. Conclusions: Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel resistance mutations to improve the design of tuberculosis control measures, such as diagnostics, and inform patient management.

Although there are many examples of color evolution potentially driven by sensory drive, only few studies have examined whether distinct species inhabiting the same environments evolve similar body colors via shared sensory mechanisms. In this study, we tested whether two sympatric freshwater fish taxa, halfbeaks of the genus Nomorhamphus and ricefishes of the genus Oryzias in Sulawesi Island, converge in both body color and visual sensitivity. After reconstructing the phylogeny separately for Nomorhamphus and Oryzias using transcriptome-wide sequences, we demonstrated positive correlations of body redness between these two taxa across environments, even after phylogenetic corrections, which support convergent evolution. However, substantial differences were observed in the expression profiles of opsin genes in the eyes between Nomorhamphus and Oryzias. Particularly, the expression levels of the long wavelength-sensitive genes were negatively correlated between the taxa, indicating ...

A major challenge in evolutionary biology is to identify the genes underlying adaptation. The oxygen-transporting haemoglobins directly link external conditions with metabolic needs and therefore represent a unique system for studying environmental effects on molecular evolution. We have discovered two haemoglobin polymorphisms in Atlantic cod populations inhabiting varying temperature and oxygen regimes in the North Atlantic. Three-dimensional modelling of the tetrameric haemoglobin structure demonstrated that the two amino acid replacements Met55β1Val and Lys62β1Ala are located at crucial positions of the α1β1subunit interface and haem pocket, respectively. The replacements are proposed to affect the oxygen-binding properties by modifying the haemoglobin quaternary structure and electrostatic feature. Intriguingly, the same molecular mechanism for facilitating oxygen binding is found in avian species adapted to high altitudes, illustrating convergent evolution in water- and air-br...

Abstract. The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + mo...

Isoenzyme-based studies have identified 3 taxa/species/' phylogenetic complexes ' as agents of visceral leishmaniasis in Sudan : L. donovani, L. infantum and '' L. archibaldi ''. However, these observations remain controversial. A new chitinase gene phylogeny was constructed in which stocks of all 3 putative species isolated in Sudan formed a monophyletic clade. In order to construct a more robust classification of the L. donovani complex, a panel of 16 microsatellite markers was used to describe 39 stocks of these 3 species. All '' L. donovani complex '' stocks from Sudan were again found to form a single monophyletic clade. L. donovani ss stocks from India and Kenya were found to form 2 region-specific clades. The partial sequence of the glutamate oxaloacetate transaminase (GOT) gene of 17 L. donovani complex stocks was obtained. A single nucleotide polymorphism in the GOT gene appeared to underlie the isoenzyme classification. It was concluded that isoenzyme-based identification is unsafe for stocks isolated in L. donovani endemic areas and identified as L. infantum. It was also concluded that the name L. archibaldi is invalid and that only a single visceralizing species, Leishmania donovani, is found in East Africa.

Isoenzyme-based studies have identified 3 taxa/species/' phylogenetic complexes ' as agents of visceral leishmaniasis in Sudan : L. donovani, L. infantum and '' L. archibaldi ''. However, these observations remain controversial. A new chitinase gene phylogeny was constructed in which stocks of all 3 putative species isolated in Sudan formed a monophyletic clade. In order to construct a more robust classification of the L. donovani complex, a panel of 16 microsatellite markers was used to describe 39 stocks of these 3 species. All '' L. donovani complex '' stocks from Sudan were again found to form a single monophyletic clade. L. donovani ss stocks from India and Kenya were found to form 2 region-specific clades. The partial sequence of the glutamate oxaloacetate transaminase (GOT) gene of 17 L. donovani complex stocks was obtained. A single nucleotide polymorphism in the GOT gene appeared to underlie the isoenzyme classification. It was concluded that isoenzyme-based identification is unsafe for stocks isolated in L. donovani endemic areas and identified as L. infantum. It was also concluded that the name L. archibaldi is invalid and that only a single visceralizing species, Leishmania donovani, is found in East Africa.

Isoenzyme-based studies have identified 3 taxa/species/‘phylogenetic complexes’ as agents of visceral leishmaniasis in Sudan: L. donovani, L. infantum and “L. archibaldi”. However, these observations remain controversial. A new chitinase gene phylogeny was constructed in which stocks of all 3 putative species isolated in Sudan formed a monophyletic clade. In order to construct a more robust classification of the L. donovani complex, a panel of 16 microsatellite markers was used to describe 39 stocks of these 3 species. All “L. donovani complex” stocks from Sudan were again found to form a single monophyletic clade. L. donovani ss stocks from India and Kenya were found to form 2 region-specific clades. The partial sequence of the glutamate oxaloacetate transaminase (GOT) gene of 17 L. donovani complex stocks was obtained. A single nucleotide polymorphism in the GOT gene appeared to underlie the isoenzyme classification. It was concluded that isoenzyme-based identification is unsafe f...

Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae), and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in d N /d S in Setophaga, implying relatively strong selective pressures to overcome long-standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark-light adaptation. Although it is unclear what these alterations mean for color perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga.

Aquatic mammals (marine and freshwater species) share significant and similar adaptations, enabling them to tolerate hypoxia during regular breath-hold diving. Despite the established importance of HIF1A, a master regulator in the molecular mechanism of hypoxia response, and other associated genes, their role in the evolutionary adaptation of aquatic mammals is not fully understood. In this study, we investigated this topic by employing a candidate gene approach to analyze 11 critical genes involved in the HIF1A signaling pathway in aquatic mammals. Our gene analyses included evaluating positive and negative selection, relaxation or constriction of selection, and molecular convergence compared to other terrestrial mammals, including subterranean mammals. Evidence of selection suggested a significant role of negative selection, as well as relaxation of the selective regime in cetaceans for most of these genes. We found that the glutamine 68 variant in the HIF3α protein is unique to c...

Domestication processes and agricultural origins were both protracted, regional processes. As these processes took many centuries, or a few millennia, they typically extended across time spans beyond that represented by any individual site and thus can be accessible to study through drawing data across multiple sites within a region. The present contribution will illustrate how agricultural origins can be understood by drawing upon evidence across multiple sites to put together a time series of quantitative data and qualitative observations. The focus here will be on cereal agriculture, setting aside the rather different processes of domestication involved with tuber-based vegecultural systems. The origins of seed crop domestication and grain-based agriculture can be illustrated with a wealth of evidence from Southwest Asia, i.e. the ancient Near East, but also with an emerging picture from evidence in sub-Saharan Africa, at both the western and eastern ends of the Sahel. The Sahelian and Near Eastern evidence provides both parallel processes but also key contrasts in terms of the nature of human settlement, sedentism versus mobility, as well as contrasting economies in terms of the importance of pastoral modes of production alongside plant food production.

Current large language models and robotic control systems face a fundamental architectural limitation: the absence of a biologically-inspired mechanism for autonomous, continuous parameter evolution. This paper draws a systematic analogy between biological epigenetic inheritance-particularly DNA methylation-driven transgenerational transmission-and the challenge of enabling silicon-based intelligent systems to autonomously consolidate experiential knowledge into persistent parametric representations. We explicitly frame this analogy as a biologically-inspired design heuristic rather than a claim of strict structural isomorphism, while identifying specific architectural constraints that apply to both biological and artificial parametric systems. We trace the evolution of robotic control from handcoded Model Predictive Control to reinforcement learning at Boston Dynamics as a motivating case study. Through analysis of transgenerational epigenetic inheritance research, including the Dias & Ressler (2014) olfactory fear conditioning study and Skinner laboratory's twenty-generation vinclozolin experiments, we identify a core biological principle: frequency-weighted probabilistic consolidation through an intermediate "shadow layer." We further identify a second consolidation pathway-intensity-driven single-event encoding mediated by adrenal stress hormones-that complements frequency-based consolidation. Building on these biological insights and engaging critically with existing continual learning approaches-including Complementary Learning Systems (CLS) theory, Elastic Weight Consolidation (EWC), progressive neural networks, and meta-learning frameworks (MAML, Reptile)we propose a layered architecture for silicon-based continuous evolution comprising three parallel base parameter modules (a core system, a reasoning layer, and a knowledge layer) overlaid by a shared shadow parameter layer. We provide a preliminary formal specification of the shadow layer update rule, consolidation threshold mechanism, and convergence conditions. The core system functions as a metaregulatory module governing evolution rules, cross-copy synchronization protocols, and value alignment-a concept we analyze in relation to the AI safety literature on value specification and corrigibility. We argue that the write-back signal from shadow layer to base parameters should follow the formula: consolidation priority = f(frequency) × g(intensity), with intensity measured by a global modulation signal emitted by the core system-directly paralleling the norepinephrine broadcast mechanism in biological memory consolidation. This framework addresses the catastrophic forgetting problem in continual learning while preserving the reconstructive, parameter-based nature of biological memory.

Octocorals possess sclerites, small elements comprised of calcium carbonate (CaCO 3 ) that are important diagnostic characters in octocoral taxonomy. Among octocorals, sea pens comprise a unique order (Pennatulacea) that live in a wide range of depths. Habitat depth is considered to be important in the diversification of octocoral species,

Two Tetramorium workers taken from a nest on the west coast of Guernsey and provisionally considered as probably T. impurum Foerster, 1850 based on existing subjective characters, are now reliably determined as that species by precise multicharacter morphometric measurements developed in a recent integrative taxonomic revision of the T. caespitum complex by Wagner and co-workers. This is the ®rst record of T. impurum from the Channel Islands and from the British Isles as a whole. The workers belong to the western clade of T. impurum in common with the population in Iberia and western France. The revision presented by Wagner and coworkers de®nes species of the T. caespitum complex, enabling a con®dent separation between T. impurum and the more abundant T. caespitum L.. The method, however, requires precision equipment and careful measurement of multiple characters. Workers with some features subjectively suggestive of T. impurum from another Guernsey locality, and from a site on Dorset heathland, are shown to be T. caespitum using the same methodology. Males of the two species present distinct qualitative character differences in genitalia morphology, enabling easier separation than by workers alone.

Annually, bacterial diarrhoea caused by Shigella spp., leads to the death of ~1.1 million people worldwide. Often overlooked, infection with Entroinvasive E. coli (EIEC), a pathogenic type of E. coli, can mimic similar dysentery-like symptoms. Shigella has been classified as a
distinct genus; however, Shigella and EIEC are closely related in genetically level. As a result, distinguishing between these two pathogens is rather challenging. Nevertheless, the distinction between EIEC and Shigella spp. is critical from a clinical or public health standpoint.
This project focuses on identifying the genes or signature sequences that can distinguish Shigella spp. and EIEC using the Genome-wide association studies (GWAS) approach. To do so, 40 isolates (20 Shigella and 20 EIEC) were sequenced. The de novo assembler was used to assemble their genomes. In addition, pre-processing tools, including trimmomatric and
FLASH, were evaluated in conjunction with the SPAdes assembler to determine their effects on the quality of assemblies. To discover distinct genetic markers, the genomes were annotated, and GWAS was performed. The core genome and SNP phylogenetic trees were
constructed to study how the isolates had evolved. Also, their serotypes and virulence genes were identified using the Serotype finder and Virulence finder. The combination of the data pre-processing method with SPAdes helped to improve the genome assemblies relatively. The greater discriminatory power of whole-genome sequencing (WGS) showed that although the genetic content of the two species is very similar (mostly
around 75-80% percentage identity), there are some subtle differences that could help differentiate the two species. Moreover, five genes: betT, betI_2, betA, betB_2, rspB, present only in EIEC, might be used as genetic markers to differentiate Shigella and EIEC. Phylogenetic analysis indicated that some Shigella spp. and EIEC had a closer connection within them than within their species, which further complicates their differentiation.
Moreover, the majority of isolates had similar virulence genes but different serotypes. GWAS had been revealed as a highly potential tool for comparative genomics. It provides high resolution while differentiating closely related species. It can be concluded that some genetic variation exists between EIEC and Shigella, which can be utilized for surveillance,
prevention, and clinical management of bacterial illnesses. To test the results' robustness, further research with a larger dataset is needed.

Most bacteria in nature live in surface-associated communities rather than planktonic populations. Nonetheless, how surface-associated environments shape bacterial evolutionary adaptation remains poorly understood. Here we show that subjecting Pseudomonas aeruginosa to repeated rounds of swarming, a collective form of surface migration, drives remarkable parallel evolution towards a hyperswarmer phenotype. In all independently evolved hyperswarmers, the reproducible hyperswarming phenotype is caused by parallel point mutations in a flagellar synthesis regulator, FleN, which locks the naturally mono-flagellated bacteria in a multi-flagellated state and confers a growth-rate independent advantage in swarming. Even though hyperswarmers outcompete the ancestral strain in swarming competitions, they are strongly outcompeted in biofilm formation, which is an essential trait for P. aeruginosa in environmental and clinical settings. The finding that evolution in swarming colonies reliably produces evolution of poor biofilm formers supports the existence of an evolutionary tradeoff between motility and biofilm formation.

During the past decade, great progress has been made in clarifying the relationships among bilaterian animals. Studies based on a limited number of markers established new hypotheses such as the existence of three superclades (Deuterostomia, Ecdysozoa, and Lophotrochozoa) but left major questions unresolved. The data sets used to the present either bear few characters for many taxa (i.e., the ribosomal genes) or present many characters but lack many phyla (such as recent phylogenomic approaches) failing to provide definitive answers for all the regions of the bilaterian tree. We performed phylogenetic analyses using a molecular matrix with a high number of characters and bilaterian phyla. This data set is built from 13 genes (8,880 bp) belonging to 90 taxa from 27 bilaterian phyla. Probabilistic analyses robustly support the three superclades, the monophyly of Chordata, a spiralian clade including Brachiozoa, the basal position of a paraphyletic Acoelomorpha, and point to an ecdysozoan affiliation for Chaetognatha. This new phylogeny not only agrees with most classical molecular results but also provides new insights into the relationships between lophotrochozoans and challenges the results obtained using high-throughput strategies, highlighting the problems associated with the current trend to increase gene number rather than taxa.

We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples of convergent evolution, we selected only those matching sites composed of structural regions whose residue order is inverted in the relative protein sequences. Results: A novel case of local analogy was detected between members of the ABC transporter and of the HprK/P families in their ATP binding site. This case cannot be derived by events of circular permutation since the residues of one of the region pairs are located in reverse order in the sequence of the two protein families. One of the analogous binding sites, the one identified in HprK/P, is known to also bind pyrophosphate, which is used as preferred energy source in its kinase and phosphorylase activity. The discovery of this striking molecular similarity, also associated to a functional similarity, may help in suggesting new experiments aimed at a deeper understanding of members of the ABC transporter family known to be involved in many serious human diseases.

The difficulty of separating genetic and ecological components of vocalizations has discouraged biologists from using vocal characters to reconstruct phylogenetic and ecological history. By considering the physics of vocalizations in terms of habitat structure, we predict which of five vocal characters of herons are most likely to be influenced by ecology and which by phylogeny, and test this prediction against a molecular-based phylogeny. The characters most subject to ecological convergence, and thus of least phylogenetic value, are first peak-energy frequency and frequency range, because sound penetration through vegetation depends largely on frequency. The most phylogenetically informative characters are number of syllables, syllable structure, and fundamental frequency, because these are more reflective of behavior and syringeal structure. Continued study of the physical principles that distinguish between potentially informative and convergent vocal characters and general patt...

Discussions of domestication and its associated genetic traits has focused upon dispersal mechanisms, for example in the rachis structure of cereals. Here we consider another trait of importance to domesticated crops – their seasonality response. We particularly consider flowering response to changing daylength, and how that relates to domesticated species that are carried by farmers considerable distances from their regions of origin. We consider the implications of cultivating crops in regions whose seasonality patterns contrast with those of the crop’s region of origin, and consider the consequent genetic changes. Reference is made to the particular case of barley, and a discussion of archaeogenetic research into its photoperiod response mechanism is provided.

Living in social groups has a range of evolutionary and ecological implications for animals. On the one hand, increased local density of conspecifics could intensify competition or make the group as a whole more visible to predators. On the other hand, social groups provide opportunities for cooperation, can potentially increase access to mating opportunities, and enable group-based antipredator mechanisms, such as increased vigilance, group defence, and dilution effects. Here, we set out to investigate the evolutionary predictors and consequences of sociality in feliform carnivorans (cats, mongooses, civets, and relatives) using a phylogenetic comparative approach. We first tested for predictors of sociality and found that sociality was more likely in larger, diurnal species which live in more open habitats, with a less slender body shape and with a more insectivorous diet. This result is consistent with the expectation from previous studies that evolution of social groups entails greater competition and ecologies that facilitate group cohesion, and perhaps are also subject to greater predation pressure. Second, we used ancestral state estimation for sociality and historical biogeographic analyses of habitats to show that sociality evolved eight times in feliforms and typically was associated with ancestral presence in or shift towards more open habitat types. Third, we investigated the consequences of sociality in terms of speciation rates and extinction risks, and found that although social species did not differ in extinction risk compared with solitary species, they did tend to have slightly lower speciation rates. Taken together, our results provide evidence for a series of costs and constraints in the evolution of sociality in mammals (e.g. in terms of competition and higher predation risk) but that these appear to be offset by the benefits provided from group-living sufficiently to avoid the longer term population consequences of higher extinction risk.

Convergent evolution is central to the study of adaptation and has been used to understand both the limits of evolution and the diverse patterns and processes which result in adaptive change. Resistance to snake venom α-neurotoxins (αNTXs) is a case of widespread convergence having evolved several times in snakes, lizards, and mammals. Despite extreme toxicity of αNTXs, substitutions in its target, the nicotinic acetylcholine receptor (nAChR), prevent αNTX binding and render species resistant. Recently, the published meerkat (Herpestidae) genome revealed that meerkats have the same substitutions in nAChR as the venom resistant Egyptian mongoose (Herpestidae), suggesting that venom-resistant nAChRs may be ancestral to Herpestids. Like the mongoose, many other species of feliform carnivores prey on venomous snakes, though their venom resistance has never been explored. To evaluate the prevalence and ancestry of αNTX resistance in mammals, we generate a dataset of mammalian nAChR utilizing museum specimens and public datasets. We find five instances of convergent evolution within feliform carnivores, and an additional eight instances across all mammals sampled. Tests of selection show that these substitutions are evolving under positive selection. Repeated convergence suggests that this adaptation played an important role in the evolution of mammalian physiology and potentially venom evolution.

Convergent evolution is central to the study of adaptation and has been used to understand both the limits of evolution and the diverse patterns and processes which result in adaptive change. Resistance to snake venom α-neurotoxins (αNTXs) is a case of widespread convergence having evolved several times in snakes, lizards, and mammals. Despite extreme toxicity of αNTXs, substitutions in its target, the nicotinic acetylcholine receptor (nAChR), prevent αNTX binding and render species resistant. Recently, the published meerkat (Herpestidae) genome revealed that meerkats have the same substitutions in nAChR as the venom resistant Egyptian mongoose (Herpestidae), suggesting that venom-resistant nAChRs may be ancestral to Herpestids. Like the mongoose, many other species of feliform carnivores prey on venomous snakes, though their venom resistance has never been explored. To evaluate the prevalence and ancestry of αNTX resistance in mammals, we generate a dataset of mammalian nAChR utili...

The repeated occurrence of similar morphologies in organisms from similar habitats provides good evidence of convergent selection, and convergent patterns of evolutionary change. In lizards, a flattened morphology has often been noted; however, whether this trait is convergent in specific habitats has never been tested using phylogenetic methods. The present study examined patterns of morphological convergence in 18 species of tropical Lygosomine skinks from three broad habitat categories (generalist, leaf litter-dwelling, and rock-using species). In general, although there where relatively few morphological differences of species from different habitats, phylogenetic analyses revealed that rock-using species have consistently and repeatedly evolved a dorsoventrally flattened head and body. The adaptive basis of this flattened morphology is consistent with both biomechanical predictions of performance (e.g. climbing locomotion) and ecology (e.g. use of rock crevices, camouflage) of species that occupy rocky habitats.