Gene sequence similarity due to shared ancestry after a duplication event, that is paralogy, complicates the assessment of genetic variation, as sequences originating from paralogs can be difficult to distinguish. These confounded sequences are often removed prior to further analyses, leaving the underlying loci uncharacterized. Salmonids have only partially rediploidized subsequent to a who…
Genetic marker-based identification of distinct individuals and recognition of duplicated individuals has important applications in many research areas in ecology, evolutionary biology, conservation biology and forensics. The widely applied genotype mismatch (MM) method, however, is inaccurate because it relies on a fixed and suboptimal threshold number (TM) of mismatches, and often yields s…
Ornithuromorpha is the most derived avian group in the Early Cretaceous, advanced members of which encompass all living birds (Neornithes). Here we report on a new basal ornithuromorph bird, Bellulia rectusunguis gen. et sp. nov., represented by a nearly complete skeleton from the Early Cretaceous Jehol Biota in northeastern China. A comprehensive phylogenetic analysis resolved the new taxon…
Understanding the classification and biosystematics of species in Triticeae Dumort., an economically important tribe in the grass family (Poaceae), is not an easy task, particularly for some perennial species. Does genomic analysis facilitate the understanding of evolutionary relationships of these Triticeae species? We reviewed literature published after 1984 to address questions concerning…
In order to trace the response of alpine plants on the Qinghai–Tibet Plateau (QTP) to the Quaternary climate oscillations, the phylogeographic history of Pomatosace filicula Maxim. was investigated in the present study. Based on sequence variations of two maternally inherited plastid markers, matK and trnH‐psbA, and the biparentally inherited nuclear ribosomal internal transcribed spacer…
Chromosome changes are common in Triticeae, and they occur widely in natural and resynthesized polyploidy. Two important factors, nucleocytoplasmic interaction (internal) and the environment (external), can significantly influence chromosome changes after polyploidization. And chromosomal DNA changes play key roles during the initial formation, gradual stabilization, and establishment of pol…
Y chromosome haplogroup O3‐M122 is the most prevalent haplogroup in East Asia, and provides an ideal tool for dissecting primary dispersals of the East Asians. Most of the sub‐haplogroups of O3‐M122 have been sufficiently investigated except for O3a1c‐002611, despite its great prevalence and huge population, especially in Han Chinese. In this study, we identified 508 individuals with h…
The southwestern Iberian Peninsula is an important biogeographic region, showing high biodiversity levels and hosting several putative glacial refugia for European flora. Here, we study the genetic diversity and structure of the Mediterranean, thermophilous plant Cheirolophus sempervirens (Asteraceae) across its whole distribution range in SW Iberia, as a tool to disentangle some of the gene…
Plants exposed to environmental stress often respond by a change in their phenotypic traits. These changes in trait expression may alleviate the negative effect of such stress factors. However, if multiple stresses are present, responses are likely to be less predictable and hence do not necessarily correlate to plant performance. This study tested if this expectation was true, by subjecting So…
Intercontinental disjunct distributions are a main issue in current biogeography. Bryophytes usually have broad distribution ranges and therefore constitute an interesting subject of study in this context. During recent fieldwork in western North America and eastern Africa, we found new populations of a moss morphologically similar to Orthotrichum acuminatum. So far this species has been cons…
Next-Generation Sequencing (NGS) technologies have revolutionized research in evolutionary biology, by increasing the sequencing speed and reducing the experimental costs. However, sequencing errors are higher than in traditional technologies and, furthermore, many studies rely on low-depth sequencing. Under these circumstances, the use of standard methods for inferring genotypes leads to biase…
Objectives: Information concerning physical growth among small-scale populations remains limited, yet such data are critical to local health efforts and to foster basic understandings of human life history and variation in childhood development. Using a large dataset and robust modeling methods, this study aims to describe growth from birth to adulthood among the indigenous Shuar of Amazonian …
The diversity and habitat requirements of invertebrates associated with dead wood have been the subjects of hundreds of studies in recent years but we still know very little about the ecological or economic importance of these organisms. The purpose of this review is to examine whether, how and to what extent invertebrates affect wood decomposition in terrestrial ecosystems. Three broad conclu…
Studies of adaptation and speciation have greatly benefited from rapid progress of DNA sequencing and genotyping technologies. Comparative genomics of closely related taxa has great potential to advance evolutionary research on genetic architecture of adaptive traits and reproductive isolation. Such studies that utilized closely related plant species and ecotypes have already provided some i…
Cell biology is a multidisciplinary scientific field that its modern expansion in new knowledge and applications owes to important support of new technologies with the rapid development, such as ICTs. By integrating knowledge from nano-, molecular, micro-, and macroareas, it represents a strong foundation for almost all biological sciences and disciplines, as well as for biomedical research and…
We have entered the Anthropocene – an era when humans are a dominant geological force – and at the same time we have entered an Urban Age. 1 Over half of humanity now lives in towns and cities, and by 2030 that fraction will have increased to 60 %. In other words, in slightly over two decades, from 2010 to 2030, another one and an half billion people will be added to the population of …
1. Savi’s pipistrelle Hypsugo savii is a Mediterranean faunal element among the bats; it occurs in southern Europe, the Canary Islands, north-western Africa, most of the Mediterranean islands, in the northern part of the Middle East, in the Crimea, Caucasus, West Turkestan, and northern Afghanistan. The northern margin of its geographical range in Europe reaches the Pyrenees, Massif Central,s…
Spinimuricea klavereni is a Mediterranean endemic gorgonian that is rarely encountered,probably because it typically occurs at depths below 50 m. It is exceptionally common in the northern Marmara Sea, with an unusually shallow upper depth limit of ~20 m. The reproductive biology of this species was studied during a one year period off B€uy€ukada, in the northeastern Marmara Sea. Spinimuric…
Polymerase chain reaction approaches for DNA sequencing from dried collection specimens of insects usually suffer from contamination, short fragment length, and limited phylogenetic power. As an alternative, we use shotgun metagenomic sequencing from mixed pools of DNA, from which mitochondrial sequences are filtered in silico. We extracted DNA from a single leg of 35 species of British butt…
Diet analysis is an important aspect when investigating the ecology of fish-eating animals and essential for assessing their functional role in food webs across aquatic and terrestrial ecosystems. The identification of fish remains in dietary samples, however, can be time-consuming and unsatisfying using conventional morphological analysis of prey remains. Here, we present a two-step multiplex …
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…