The black-lip pearl oyster Pinctada margaritifera is a protandrous hermaphrodite species. Its economic value has led to the development of controlled hatchery reproduction techniques,although many aspects remain to be optimized. In order to understand reproductive mechanisms and their controlling factors, two independent experiments were designed to test hypotheses of gametogenesis and sex rati…
Mammalian dental morphology is under strong evolutionary pressure because of its importance for mastication and diet. While the mechanisms underlying tooth development have been widely studied in model organisms, the role of genetic regulatory elements in patterning the different elements of the occlusal surface and crown height across species is not well understood. Previous studies showed …
The early evolution of Amphisbaenia has received much attention from researchers (Kearney & Stuart 2004; Townsend et al. 2004; M€uller et al. 2011), but the origin of this group remains poorly understood. Phylogenetic analyses have yielded conflicting results regarding their relationships with other squamates (Conrad 2008; Gauthier et al. 2012; Wiens et al. 2012). Analyses using molecular …
Comparison of the genomes of different Drosophila species has shown that six different chromosomes, the so-called ‘‘Muller elements,” constitute the building blocks for all Drosophila species. Here, we confirm previous results suggesting that this conservation of the Muller elements extends far beyond Drosophila, to at least tephritid fruit flies, thought to have diverged from drosophilid…
Recent molecular phylogenetic studies on Elymus have added to our understanding of the origination of Elymus species. However, evolutionary dynamics and speciation of most species in Elymus are unclear. Molecular phylogeny has demonstrated that reticulate evolution has occurred extensively in the genus, as an example, the largest subunit of RNA polymerase II (rpb2) and phosphoenolpyruvate ca…
Clarification of the metabolic mechanisms underlying multi-stress responses in plants will allow further optimisation of crop breeding and cultivation to obtain high yields in an increasingly variable environment. Using NMR metabolomic techniques, we examined the metabolic responses of maize plants grown under different conditions:soil drought, soil salinity, heat and multiple concurrent stress…
The Qinghai–Tibet Plateau (QTP) is the highest and largest plateau in the world. It covers correspondingly wide geological, topographical, and climatic gradients, and thus hosts greater biodiversity than surrounding lowlands and other high elevation regions. Due to its extreme environmental and biological diversity, the QTP is an ideal region for studying adaptations of plant species under h…
Fishes are particularly sensitive to the effects of environmental conditions during early development,which can significantly impact adult morphology, performance, and survival. Previous research has highlighted the sensitivity of fishes to the effects of temperature during early development on vertebral number and muscle composition, which are both important determinants of an individual's swi…
Pest management requires the development of robust monitoring tools. In Italy,coypu Myocastor coypus (nutria) have been controlled since the early 1990s,but the effectiveness of these measures has never been tested. With the aim of developing a reliable and volunteer-based method for the long-term monitoring of coypu abundance in agricultural landscapes, we calibrated an index based on surveys…
Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organe…
Museums hold most of the world’s most valuable biological specimens and tissues collected, including type material that is often decades or even centuries old. Unfortunately, traditional museum collection and storage methods were not designed to preserve the nucleic acids held within the material, often reducing its potential viability and value for many genetic applications. High-throughp…
Objectives: This study explored the developmental trajectory of aggressive behavior from age 8 to age 10 in schoolaged children, taking into account possible sex differences, as well as the involvement of certain hormones. Methods: Participants were 90 children (49 boys and 41 girls) from four schools. At the beginning of the study, the children were 8-year old and were in 3rd grade of primar…
Flowering is a key life-history event whose timing almost certainly affects both male and female fitness, but tests of selection on flowering time through male fitness are few. Such selection may arise from direct effects of flowering time, and indirect effects through covariance between flowering time and the environment experienced during reproduction. To isolate these intrinsically correlate…
1. Vegetation structure is an important determinant of species habitats and diversity. It is often represented by simple metrics, such as canopy cover, height and leaf area index, which do not fully capture three-dimensional variations in density. Terrestrial laser scanning (TLS) is a technology that can better capture vegetation structure, but methods developed to process scans have been bi…
1. A subdiscipline of conservation science involves the study of differences between threatened and non-threatened species. The relevance of multispecies analyses of extinction risk to conservation practice has been questioned, but there has been no synthesis of the allocation of research effot to different regions and groups of mammals to assess whether or not sufficient knowledge is available…
Similar to seemingly maladaptive genes in general, the persistence of inherited cancer-causing mutant alleles in populations remains a challenging question for evolutionary biologists. In addition to traditional explanations such as senescence or antagonistic pleiotropy, here we put forward a new hypothesis to explain the retention of oncogenic mutations. We propose that although natural defens…
1. The analysis ofmorphological diversity frequently relies on the use ofmultivariate methods for characterizing biological shape. However, many of these methods are intolerant of missing data, which can limit the use of rare taxa and hinder the study of broad patterns of ecological diversity and morphological evolution. This study applied a mutli-data set approach to compare variation in mi…
The ash leaf cone roller Caloptilia fraxinella Ely (Lepidoptera: Gracillariidae)is an invasive leaf-mining moth pest of horticultural ash Fraxinus spp. in the Canadian Prairie Provinces. Caloptilia fraxinella overwinter as adults in reproductive diapause and mating occurs after overwintering in the spring. The effect of a carbohydrate food source on fat and glycerol reserves throughout the lon…
1. Molecular clock calibration is a crucial step for placing phylogenetic trees in the temporal framework required to test evolutionary hypotheses and estimate evolutionary rates. In general, most authors agree that the best approach is to incorporate multiple calibrations to avoid the risk of bias associated with a single dating source. However, the indiscriminate inclusion of as many calib…
The objective of this paper is to summarize the work in my group on FISH (fluorescent in situ hybridization) mapping of Ns‐specific repetitiveDNAsequences from Leymus and discuss the results in the context of classification based on the genome system currently used among Triticeae researchers. The key question here is whether the genome composition of a tetraploid Leymus species should be NsX…
Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild…
A central goal of evolutionary biology is the understanding of the processes that result in morphological and genetic diversity. Land snails were often used as model organisms for evaluating the roles of selection and history in the origins of biodiversity (Davison 2002). In particular notable are the classical studies of Cepaea that nicely illustrated the action and effects of natural select…
Brown citrus aphid Toxoptera citricida Kirkadly is considered as an important pest of citrus because it vectors citrus tristeza closterovirus. Aphids secrete a fluid from their cornicles as a defensive mechanism against natural enemies. Earlier studies on cornicle secretions of aphids focus only on triglycerides and fatty acids. In the present study, three different methods are used to investi…
1. Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but usingRcan be challenging for many researchers due to its steep learning curve. 2. POPGENREPORT is a new R package that simplifies performing population genetics analyses in R, through the use of a new report-generating function. The function POPGENREPORT allows users…
Abstract. Little is known about the reproductive biology of corals from the Philippines,despite this archipelago being at the center of coral reef biodiversity. Here, we report on the reproductive biology of a branching poritid species provisionally identified as Porites cf. cylindrica in the Bolinao-Anda reef complex (BARC), northwestern Philippines. Histological examination and ex situ planul…
Human height is a highly variable trait, both within and between populations, has a high heritability, and influences the manner in which people behave and are treated in society. Although we know much about human height, this information has rarely been brought together in a comprehensive, systematic fashion. Here, we present a synthetic review of the literature on human height from an expl…
A new chroococcalean cyanobacterium is described from approximately 1-billion-year-old non-marine deposits of the Torridonian Group of Scotland and the Nonesuch Formation of Michigan, USA. Individual cells of the new microfossil, Eohalothece lacustrina gen. et sp. nov., are associated with benthic microbial biofilms, but the majority of samples are recovered in palynological preparations in the…
Obtaining biological and spatial information of the early life history (ELH) phases of fishes has been problematic, such that larval and juvenile phases are often referred to as the ‘black box’ of fish population biology and ecology. However, a potent source of life-history data has been mined from the earstones (otoliths) of bony fishes. We systematically reviewed 476 empirical papers publ…
Romer’s Gap, the interval following the end-Devonian extinction event, has been described as a post-extinction trough for vertebrates. It is a time roughly equivalent to the Tournaisian stage of the early Carboniferous and has been characterized by a lull in diversity of survivors. Lungfish typified this description. One species was known from one locality. Recently, a diverse collection of…
This review examines two classes of organism that live in symbiosis; grasses, and fungi. Specifically it deals with grasses of the tribe Hordeeae (formerly Triticeae) of the subfamily Poöideae and the Epichloë fungi of family Clavicipitaceae. Epichloë endophytes, particularly asexual forms, have important roles in pastoral agricultural systems in the Americas, Australia, and New Zealand. Se…
Objectives: To analyze the relationship between different physical activity (PA) domains and sociodemographic, psychological,behavioral and biological factors in Brazilian adolescents. Methods: 1,220 adolescents (55.1% female) aged between 10 and 16 years-old participated in this study. The Baecke questionnaire was used to evaluate different PA domains, namely occupational, sports and leisure…
Osmoregulation, respiration, nutrient/mineral transport, and defense mechanisms are all evident in the integument of fish. The role of the integument in these physiological processes is particularly important during early life history in larval fishes, as functional systems such as the gills and gastrointestinal tract are not fully developed. Using a variety of microscopy techniques, we describ…
Abundant, exquisitely preserved specimens of the enigmatic tubular microfossil Megathrix longus are reported from the early Cambrian Yanjiahe Formation in the Yangtze Gorges area. Studies of their morphology and taphonomy reveal that the inner cross-wall of Megathrix longus is topographically flat, the trichome terminus is blunt and closed, and incomplete cross-walls are regularly intercalate…
The contractile protein myosin II is ubiquitous in muscle. It is widely accepted that animals express tissue-specific myosin isoforms that differ in amino acid sequence and ATPase activity in order to tune muscle contractile velocities. Recent studies, however, suggested that the squid Doryteuthis pealeii might be an exception; members of this species do not express muscle-specific myosin isof…
Leymus Hochst. is a polyploid genus with a diverse array of morphology, cytology, ecology, and distribution in Triticeae. To investigate the phylogenetic relationships and maternal genome donor of polyploid Leymus, the chloroplast trnH‐psbA region and mitochondrial coxII intron sequences of 33 Leymus taxa were analyzed with those of 36 diploid perennial species representing 19 basic genome…
IMa2 and related programs are used to study the divergence of closely related species and of populations within species. These methods are based on the sampling of genealogies using MCMC, and they can proceed quite slowly for larger data sets. We describe a parallel implementation, called IMa2p, that provides a nearly linear increase in genealogy sampling rate with the number of processors in …
Population genetic studies of widespread Mediterranean shrubs are scarce compared with those of trees and narrow endemics or studies from phylogeographical perspectives, despite the key role these species may play in Mediterranean ecosystems. Knowledge on the effect of ecological factors in shaping their genetic patterns is also limited. In this study we investigate genetic diversity and pop…
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Pa…
Hybridization between closely related species, whether naturally occurring or laboratory generated, is a useful tool for mapping the genetic basis of the phenotypic traits that distinguish species. The development of next-generation sequencing techniques has greatly improved our ability to assign ancestry to hybrid genomes. One such next-generation sequencing technique, multiplexed shotgun g…
This overview summarizes the current situation, history, major controversies, and medical implications of scientific biological aging theories. See Further Reading for a much more comprehensive treatment of this subject.
Bone is a specialized connective tissue, most prominently characterized by its mineralized organic matrix that imparts the physical properties that allow bone tissue to resist load, to support functional organs, and to protect highly sensitive body parts. Bone loss and bone damage may occur as a result of genetic conditions, infectious diseases, tumours, and trauma. Bone healing and repair, inv…
1. Research addressing the role of epigenetics in a diversity of experimental and natural systems is rapidly accumulating. Diverse methods have been developed to study epigenetic states, including bisulphite sequencing and AFLP-based approaches. However, existing methods are sometimes difficult to apply to non-traditional model organisms that lack genomic resources (bisulphite sequencing), a…
We provide a detailed anatomical description of the skull of the fossil minute boas Messelophis variatus Baszio, 2004 and Messelophis ermannorum Schaal & Baszio, 2004 from the Middle Eocene Messel Formation (Germany), as well as a cladistic analysis to infer their phylogenetic relationships. Reanalysis of new and known specimens of both species demonstrates previously unrecognized anatomical…
Despite the complexity of nature, most comparative studies of phenotypic evolution consider selective pressures in isolation. When competing pressures operate on the same system, it is commonly expected that trade-offs will occur that will limit the evolution of phenotypic diversity, however, it is possible that interactions among selective pressures may promote diversity instead. We explored t…
Adaptive radiations are major contributors to species diversity. Although the underlying mechanisms of adaptive radiations,specialization and trade-offs, are relatively well understood, the tempo and repeatability of adaptive radiations remain elusive. Ecological specialization can occur through the expansion into novel niches or through partitioning of an existing niche. To test how the mode o…
The opisthotonic (‘dead bird’) posture encountered in non-avialan dinosaurs and other fossilized archosaurs is characterized by extreme dorsal neck retraction and tail protraction. Extant birds have been used to study this and attention has focused on the neck (because modern avians lack a long, freely articulated series of caudal vertebrae). The opisthotonic posture has been largely discus…
1. Capture–recapture studies are often conducted on populations that are stratified by space, time or other factors. In this paper, we develop a Bayesian spatial capture–recapture (SCR) modelling framework for stratified populations – when sampling occurs within multiple distinct spatial and temporal strata. 2. We describe a hierarchical model that integrates distinct models for both t…
Objectives: Little is known about cannabis use in hunter-gatherers. Therefore, we investigated cannabis use in the Aka, a population of foragers of the Congo Basin. Because cannabis contains anthelminthic compounds, and the Aka have a high prevalence of helminthiasis, we also tested the hypothesis that cannabis use might be an unconscious form of self-medication against helminths. Methods: W…
Abstract—Essential proteins are vital for an organism’s viability under a variety of conditions. There are many experimental and computational methods developed to identify essential proteins. Computational prediction of essential proteins based on the global protein-protein interaction (PPI) network is severely restricted because of the insufficiency of the PPI data, but fortunately the ge…
Objectives: We conduct a revaluation of the Thornhill and Fincher research project on parasites using finelyresolved geographic data on parasite prevalence, individual-level sociocultural data, and multilevel Bayesian modeling. In contrast to the evolutionary psychological mechanisms linking parasites to human behavior and cultural characteristics proposed by Thornhill and Fincher, we offer a…