Parallelism in Endocarp Form Sheds Light on Fruit Syndrome Evolution in Viburnum

Abstract— All Viburnum species produce drupes with a hardened endocarp surrounding a single seed. Endocarp form varies greatly within Viburnum, and differences in shape have long been used to distinguish major subclades. Here we trace the evolution of Viburnum endocarp shape using morphometric analyses and phylogenies for 115 Viburnum species. Endocarp measurements were obtained from fruits sampled from herbarium specimens and from field collections, and shapes were analyzed using elliptical Fourier analysis. We infer that the first viburnums had flattened and grooved endocarps. Subsequently, there were multiple losses of grooving in conjunction with shifts to both highly flattened and nearly round endocarps. In several clades the parallel evolution of a derived endocarp shape was accompanied by changes in a suite of other fruit traits, yielding distinctive fruit syndromes likely related to bird dispersal. However, in other clades endocarp shapes similar to the ancestral form have been retained while other fruit traits (color, amount of flesh, nutritional content) have diverged. We quantify cases of parallel evolution in endocarp shape that cut across recognized fruit syndromes such as red, carbohydrate-rich fruits with flattened endocarps or blue, lipid-rich fruits with round endocarps. Our analyses now invite studies of function and the selective factors that have yielded the distinctive suites of fruit and seed traits that distinguish the major Viburnum lineages.

A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism

Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide–reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca.) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.

Genomic insights into the recent chromosome reduction and polyploidization of complex autopolyploid sugarcane S. spontaneum

S. spontaneum is a founding Saccharum species that contributes stress resistance to the genetic background of modern sugarcane cultivars. Here, we have assembled the autopolyploid S. spontaneum Np-X genome with ancestral form into 40 pseudo-chromosomes in 10 homologous groups, revealing the recent chromosome reduction and polyploidization that occurred in Saccharum. The paleo-duplicated chromosomal pairs exhibit functional redundancy in Saccharum and underwent fission followed by fusion accompanied by centromeric spreading around 0.80 million years ago (Mya) before evolving into their current forms with basic chromosome numbers x = 9 and x = 8 in S. spontaneum, likely in a stepwise manner. WGDs occurred independently in Saccharum species around 1.5 Mya. Highly diverse chromatin structures exist among homologous chromosomes despite their high collinearity, and the re-structuring of NpChr5 and NpChr8 might have suppressed switching of chromatin structure from inactive to active. Resequencing of 116 sugarcane accessions elucidated that the S. spontaneum originated from North India and that the basic chromosome numbers x = 8, x = 9, and x = 10 originated independently, indicating that recent chromosome reduction rather than polyploidization has driven the adaptive evolution of Saccharum. Our study provides genomic resources and suggests new directions for accelerating sugarcane improvement and advances our knowledge of the evolution of auto-polyploids.

Population genetic analysis of Fagus orientalis Lipsky from the territory of the Crimea and the Caucasus

The genetic structure of 20 populations of Fagus orientalis Lipsky (oriental beech) from the territory of the Crimea and the Caucasus was studied on the basis of microsatellite polymorphism (SSR – simple sequence repeats). The isolation distance test performed in the GenePop program showed a high correlation of genetic differences and the logarithm of geographic distance in geographic coordinates at the 0.91 level. Interpopulation genetic differentiation of Fagus orientalis (Fst) ranged from 0.01 to 0.67. On the basis of the obtained genetic data and analysis of the literature on fossil materials, we present a preliminary reconstruction of the possible pathways for spread and the formation of the modern area of the species in the Crimea and on the Caucasian Isthmus within the Caucasian ecoregion. The earliest separation occurred in the populations of the mountainous Crimea and the Stavropol Upland, which retained the unique features of the genotype of the ancestral form in conditions of island isolation. Apparently, beeches from relict mid-mountain populations in refugia of mesophilic vegetation are close to the ancestral form: Colchis (Avadhara, Abkhazia) in the west and Kakheti (Lagodekhi, Georgia) in the east. The observed similarity at the upper border of the beech belt in different regions of the Caucasian Isthmus indicates a parallelism in the development and formation of high-mountain populations of the species.

The fusion peptide proximal region of the HIV-1 envelope glycoproteins regulates exposure of immunogenic epitopes at the trimer base

ABSTRACTThe error-prone replication machinery of HIV-1 continuously generates new variants of the envelope glycoproteins (Envs). Antibody selection pressures applied in the host can limit their persistence. The target specificity of antibodies elicited in different hosts varies considerably. Whether some specificities are shared and have affected the population-level evolution of Env structure is still unclear. We examined the historical changes in amino acid sequence of the gp41 fusion peptide proximal region (FPPR), which is not exposed on the Env trimer. For three FPPR positions, the residue found in the clade B ancestor was mainly replaced by alanine. However, the changes in alanine frequency at these positions between 1979 and 2016 followed different patterns; two positions maintained a historically-constant frequency whereas the third showed a gradual increase. To understand these patterns, we introduced alanine substitutions in the FPPR of primary HIV-1 strains and examined their fitness and antigenicity relative to the clade-ancestral form. The evolutionary patterns could not be explained by effects on Env fitness. Instead, the FPPR variants with a historically-constant alanine frequency exhibited a unique open-at-the-base conformation of the trimer that exposes partially-cryptic epitopes. These Envs were modestly but significantly more sensitive to poorly-neutralizing sera from HIV-infected individuals than the clade-ancestral form. Our findings suggest that weakly-neutralizing antibodies targeting the base of the trimer are commonly elicited. Such low-level antibody pressures do not exert catastrophic effects on the emerging variants but rather determine their set-point frequency in the population and historical patterns of change.IMPORTANCEHIV-1 infection elicits antibodies that target the Env proteins of the virus. The specific targets of these antibodies vary between infected individuals. It is unclear whether some target specificities are shared between the antibody responses of different individuals. Our data suggest that antibodies against the base of the Env protein are commonly elicited during infection and are contained in sera with low neutralization efficacy. Such antibody pressures are weak. As a result, they do not completely eliminate the sensitive Env forms from the population, but rather maintain their frequency at a low level that has not increased during the past 40 years.

Comparisons of Respiratory Pupal Gill Development in Black Flies (Diptera: Simuliidae) Shed Light on the Origin of Dipteran Prothoracic Dorsal Appendages

During the transformation of immature aquatic dipteran insects to terrestrial adults, the prothoracic pupal respiratory organ enables pupae to cope with flood-drought alternating environments. Despite its obvious importance, the biology of the organ, including its development, is poorly understood. In this study, the developing gills of several Simulium Latreille (Diptera: Simuliidae) spp. were observed using serial histological sections and compared with data on those of other dipteran families published previously. The formation of some enigmatic features that made the Simulium gill unique is detailed. Through comparisons between taxa, we describe a common developmental pattern in which the prothoracic dorsal disc cells not only morph into the protruding respiratory organ, which is partially or entirely covered with a cuticle layer of plastron, but also invaginate to form a multipart internal chamber that in part gives rise to the anterior spiracle of adult flies. The gill disc resembles wing and leg discs and undergoes cell proliferation, axial outgrowth, and cuticle sheath formation. The overall appendage-like characteristics of the dipteran pupal respiratory organ suggest an ancestral form that gave rise to its current forms, which added more dimensions to the ways that arthropods evolved through appendage adaptation. Our observations provide important background from which further studies into the evolution of the respiratory organ across Diptera can be carried out.

The differential diversification of Mongolic

This paper examines the Mongolic family of languages from the point of view of their different paths and rates of evolution, and with a view on the general problem concerning the speed of language change. All extant Mongolic languages descend from a relatively recent ancestral form of speech, Proto-Mongolic, spoken by the historical Mongols in the twelfth to fourteenth centuries and documented in a number of written sources conventionally known as Middle Mongol. A comparison of the modern Mongolic languages with Proto-Mongolic and Middle Mongol reveals considerable differences in their rates of evolution, with some languages being highly innovative, while others are conspicuously conservative. These differences are evident at all levels of linguistic structure and substance, including phonology, grammar, and lexicon. The reasons for the different rates of evolution can be sought in a variety of linguistic and extralinguistic factors, including not only the linguistic environment, but also the political and geographical context of the speakers, as well as their demographic structure, economic and cultural profile, and degree of mobility.

Adaptability and evolution of the cell polarization machinery in budding yeast

SummaryHow can a self-organized cellular function evolve, adapt to perturbations, and acquire new sub-functions? To make progress in answering these basic questions of evolutionary cell biology, we analyze, as a concrete example, the cell polarity machinery of Saccharomyces cerevisiae. This cellular module exhibits an intriguing resilience: it remains operational under genetic perturbations and recovers quickly and reproducibly from the deletion of one of its key components. Using a combination of modeling, conceptual theory, and experiments, we show that multiple, redundant self-organization mechanisms coexist within the protein network underlying cell polarization and are responsible for the module’s resilience and adaptability. Based on our mechanistic understanding of polarity establishment, we hypothesize how scaffold proteins, by introducing new connections in the existing network, can increase the redundancy of mechanisms and thus increase the evolvability of other network components. Moreover, our work suggests how a complex, redundant cellular module could have evolved from a more rudimental ancestral form.

Palenquero origins

Palenquero is a Spanish-lexified creole spoken in Columbia. We argue that existing hypotheses regarding its birth are problematic in several regards. This article addresses the inconsistencies in these hypotheses and provides an alternative, more coherent account. More precisely, we take issue with the following three claims: (a) Palenquero is the result of a two-language encounter; (b) it has its roots in a West African Afro-Portuguese proto-variety; (c) an ancestral form of the creole emerged in the port city of Cartagena. We then set out to present our own, more economical, formation scenario, according to which Palenquero was formed in the early 1600s in the linguistically heterogenous maroon communities of the Cartagenan hinterlands.

A Study of DOM in Asturian (‘Dialectu Vaqueiru’)

The present paper explores Differential Object Marking in a variety of Asturian (Western Iberian Romance) spoken in western Asturias (northwestern Spain). This ancestral form of speech stands out from Central Asturian and especially from Standard Spanish. For a number of reasons, ranging from profound changes in pronunciation, vocabulary, morphology and information structure to slight but very relevant effects on syntax. The main goal of this study is to examine the special marking of direct objects in order to find out what triggers the distribution of Differential Object Marking in this variety. To this aim, this paper will examine, from a variationist perspective, the influence of a number of semantic and discourse-pragmatic parameters on the marking of direct objects in this Western Asturian language as well as in Standard Spanish 1 and Central Asturian (which is generally considered the normative variety of Asturian). The results obtained from this comparison will allow us to outline the differences between these three varieties in terms of object marking, shedding more light on the origin and function of Differential Object Marking in Spanish.