Concrete examples help to understand complex systems. In this report, the key point is to illustrate the basic mechanisms and properties of neocybernetic system models. Good visualizations are certainly needed. It is biological systems, or living systems, that are perhaps the most characteristic examples of cybernetic systems. This intuition is extended here to natural systems in general —…
The evolution of the middle ear from the cynodont craniomandibular bones is one of the key mammalian innovations, and the mechanics underlying this anatomical transformation represents an intriguing paradox. Because the jaw joint of nonmammalian cynodonts was functionally coupled to the inner ear, auditory performance would favor low joint reaction forces. However, this could not be achieved at…
The evolution of the middle ear from the cynodont craniomandibular bones is one of the key mammalian innovations, and the mechanics underlying this anatomical transformation represents an intriguing paradox. Because the jaw joint of nonmammalian cynodonts was functionally coupled to the inner ear, auditory performance would favor low joint reaction forces. However, this could not be achieved at…
1. In the face of natural complexities and multicollinearity, model selection and predictions using multiple regression may be ambiguous and risky. Confounding effects of predictors often cloud researchers’ assessment and interpretation of the single best ‘magicmodel’. The shortcomings of stepwise regression have been extensively described in statistical literature, yet it is still widely…
Alternative energy sources have become a hot topic in recent years. The supply of fossil fuel, which provides about 95 percent of total energy demand today, will eventually run out in a few decades. By contrast, biomass and biofuel have the potential to become one of the major global primary energy source along with other alternate energy sources in the years to come. A wide variety of biomass …
Objectives: The association between blood levels of hemoglobin (B-hgb) and blood pressure (BP) has been widely investigated in Caucasians and Asians but there is a paucity of data in rural black Africans. The objective was to investigate the association between B-hgb and BP in a rural black African population. Methods: A cross-sectional study was conducted in three districts in Kenya (Bondo, K…
Time-calibrated phylogenies that contain only living species have been widely used to study the dynamics of speciation and extinction. Concerns about the reliability of phylogenetic extinction estimates were raised by Rabosky (2010), where I suggested that unaccommodated heterogeneity in speciation rate could lead to positively biased extinction estimates. In a recent article,Beaulieu and O’M…
Ecologists frequently use a supertree method to generate phylogenies in ecological studies. However, the robustness of research results based on phylogenies generated with a supertree method has not been well evaluated. Here, we use the angiosperm tree flora of North America as a model system to test the robustness of phylogenies generated with a supertree method for studies on the relations…
Fothergilla (Hamamelidaceae) consists of Fothergilla gardenii (4x) from the coastal plains of the southeastern USA, F. major (6x) from the piedmont and mountains of the same region, and a few allopatric diploid populations of unknown taxonomic status. The objective of this study was to explore the relationships of the polyploid species with the diploid plants. Genotyping by sequencing (GBS) …
The topics of succession and post-disturbance ecosystem recovery have a long and convoluted history. There is extensive redundancy within this body of theory, which has resulted in confusion, and the links among theories have not been adequately drawn. This review aims to distil the unique ideas from the array of theory related to ecosystem change in response to disturbance. This will help to r…
The year 2014 marked the 25th International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in G€ottingen,Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published.Wepresent herein a citational network analysis of these papers, and touch on some of the import…
In the last decade, taxonomic studies have drastically increased the number of species known to inhabit the Arabian deserts. While ongoing phylogenetic studies continue to identify new species and high levels of intraspecific genetic diversity, few studies have yet explored the biogeographic patterns in this arid region using an integrative approach. In the present work, we apply different phyl…
1. Predicting space use patterns of animals from their interactions with the environment is fundamental for understanding the effect of habitat changes on ecosystem functioning. Recent attempts to address this problem have sought to unify resource selection analysis,where animal space use is derived from available habitat quality, andmechanistic movement models, where detailedmovement proces…
Prerequisites for conservation planning are inventories of species, which are often recognised and described using morphological clues (The House of Lords 2003; The Royal Society 2003; Mace 2004). However, taxa identification using morphological criteria may be challenging, especially in simple organisms that present few discriminant synapomorphies and high phenotypic plasticity, such as cni…
Amniote vertebrates, the group consisting of mammals and reptiles including birds, possess various mechanisms of sex determination. Under environmental sex determination (ESD), the sex of individuals depends on the environmental conditions occurring during their development and therefore there are no sexual differences present in their genotypes. Alternatively, through the mode of genotypic …
The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencin…
We defined the somatic environment in which female germinal cells develop, and performed ultrastructural analyses of various somatic cell types, with particular reference to muscle cells and follicle cells, that reside within the ovary at different stages of oogenesis. Our findings show that ovarian wall of the crayfish is composed of long muscle cells, blood cells, blood vessels and hemal s…
Plant sexual systems can be affected by various environmental factors, and thus show a range of morphological differences. The associations between plant sexual systems and morphology are unique, for example, the subnival belt of the Hengduan Mountains has harsh climatic conditions, but hosts remarkable biodiversity. However, these associations have received surprisingly little attention. We…
1. Current developments of diversity measures that consider that species are not equivalent, concentrate on how functionally or phylogenetically (dis)similar species are from each other (interspecific components). To assess the biodiversity of a community, few of the developed measures include intraspecific components, that is to say components that concern only the current features of the in…
Debates about how coevolution of sexual traits and preferences might promote evolutionary diversification have permeated speciation research for over a century. Recent work demonstrates that the expression of such traits can be sensitive to variation in the social environment. Here, we examined social flexibility in a sexually selected male trait—cuticular hydrocarbon (CHC) profiles—in the …
Objective: Here we evaluate morphological integration patterns and magnitudes in different skull regions to detect if shifts in morphological integration are correlated to the appearance of more processed (softer) diets. Methods: To do so, three transitional populations were analyzed, including samples from groups that inhabited the same geographical region and for which the evidence shows t…
Evolutionary theory for expenditure on gonads attracted little attention until studies in the past 3–4 decades of allocation to male and female function in hermaphrodites, and of relative testes size (RTS) in animals with separate sexes. RTS appears to have varied enormously over evolutionary time, from extremely high (over 40%) in some broadcast spawners to less than 1% in some taxa with co…
1. Functional diversity (FD) is an important concept for studies of both ecosystem processes and community assembly, so it is important to understand the behaviour of common metrics used to express it. 2. Data from an existing study of the relationship between FD and environmental drivers were used to simulate the impact of a progressive failure to measure the traits of all the species prese…
By combining high-throughput sequencing with target enrichment (‘hybridization capture’), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization …
The ever-increasing number of studies that address the origin and evolution of Euarthropoda – whose extant representatives include chelicerates, myriapods, crustaceans and hexapods – are gradually reaching a consensus with regard to the overall phylogenetic relationships of some of the earliest representatives of this phylum. The stem-lineage of Euarthropoda includes numerous forms that r…
1. Radiotelemetry and satellite-based telemetry approaches are essential to describe the behaviour and biology of animals. This is especially true for bats, whose small size and cryptic lifestylesmake themchallenging to study. However, only a handful of studies have evaluated how transmitter mass and the attachment method affect bat behaviour or health, and none have assessed the development…
Recent studies have demonstrated adaptive evolutionary responses to climate change, but little is known about how these responses may influence ecological interactions with other organisms, including natural enemies.We used a resurrection experiment in the greenhouse to examine the effect of evolutionary responses to drought on the susceptibility of Brassica rapa plants to a fungal pathogen, Al…
1. Telomeres play a fundamental role in the protection of chromosomal DNA and in the regulation of cellular senescence. Recent work in human epidemiology and evolutionary ecology suggests adult telomere length (TL) may reflect past physiological stress and predict subsequent morbidity and mortality, independent of chronological age. 2. Several differentmethods have been developed to measure…
Nearctic taxa, which jointly colonized Eurasia and the Maghreb during the Miocene. The strict trophic relationships occurring between the glossiphoniid parasite leech Placobdella costata and its host, the emydid Emys orbicularis, make them a prime example of host–parasite cophylogenetic evolution. In the light of the discovery of the Sicilian cryptic endemic species Emys trinacris, which is t…
Cavitated secretory trichomes are characterized by a short or absent stalk that is connected to a secretory hollow head. They are rare structures in angiosperms; in Fabaceae, they have been recorded in only seven genera, including Bauhinia s.s. Because B. curvula and B. rufa exhibit glands that are responsible for attracting pollinators to flowers, this study aimed to test whether the cavita…
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and…
Next-generation sequencing and phylogenomics hold great promise for elucidating complex relationships among large plant families. Here, we performed targeted capture of low copy sequences followed by nextgeneration sequencing on the Illumina platform in the large and diverse angiosperm family Compositae (Asteraceae). The family is monophyletic, based on morphology and molecular data, yet many…
Hypogean habitats offer unique opportunities for ecological studies because they are characterized by low abundance and diversity of organisms, they receive low energy inputs, they are relatively stable from a climatic point of view, and they are quite easily modeled. However, given the harsh conditions of the working environment and difficulty of access, very few studies have investigated in …
With the advance of next-generation sequencing techniques, phylogenetic analyses based on genomic data are becoming frequent in plants. However, the efficacy of different methods used to retrieve orthologs for phylogenetic studies based on transcriptome sequences is rarely compared and examined for closely related species with low genetic differentiation. In this study, we used both low-copy ge…
Mammalian enamel, the contact dental tissue,is something of an enigma. It is almost entirely made of hydroxyapatite, yet exhibits very different mechanical behavior to a homogeneous block of the same mineral. Recent approaches suggest that its hierarchical composite form,similar to other biological hard tissues, leads to a mechanical performance that depends very much on the scale of measuremen…
Effective conservation of crop wild relative (CWR) species is essential for the sustainable use and genetic improvement of crop varieties, which offers greater opportunities for world food security, particularly in modern agroecosystems where CWR diversity is under severe threat. Factors such as habitat fragmentation, human disturbances, global climate change, and invasion of harmful alien s…
Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep …
Miniature inverted repeat transposable elements (MITEs) are the most ubiquitous transposable elements in eukaryotic genomes; they play a prominent role in sequence divergence and genome evolution. There are many wellcharacterized Stowaway‐like MITE families in wheat, but their distribution, abundance, and composition at the chromosome level are still not well understood. In this study, we sys…
It remains unknown how Ostryopsis intermedia B. Tian & J. Q. Liu (Betulaceae) originated in the SE Qinghai–Tibet Plateau (QTP). We examined sequence variations of two maternally inherited chloroplast (cp) DNA fragments and amplified fragment length polymorphisms (AFLP) of 32 populations for this species and two congeners, O. davidiana Decne. and O. nobilis Balf. f. W. W. Sm., distributed i…
Linguistics and genetics always reach similar results in phylogenetic studies of human populations. A previous study found that populations speaking Han Chinese dialects have closer genetic relationships to each other than to neighboring ethnic groups. However, the Pinghua Chinese population from Guangxi is an exception. We have reported that northern Pinghua people are genetically related to p…
Unionoid freshwater mussels have a unique life cyclewith a form of parental care where the larvae are developed and kept inside the gills until release, followed by an obligate parasitic stage on fish. The size and location of the marsupium have been used as important phylogenetic characters in unionoids and in Anodontini its location was described exclusively on the outer demibranchs. Two rece…
The late Ediacaran siliciclastic successions of eastern Newfoundland, Canada, are renowned for their fossils of soft-bodied macro-organisms, which may include some of the earliest animals. Despite the potential importance of such fossils for evolutionary understanding, the taxonomic framework within which Ediacaran macrofossils are described is not clearly defined. Rangeomorphs from a newly di…
Mate, prey, and predator recognition often depend on the integration of information from multiple sensory modalities including visual, auditory,and/or olfactory inputs. In Crotalinae, the eyes sense visible light while the pit organs detect infrared (IR) radiation. Previous studies indicate that there is significant overlap between the eye and pit sensory fields and that both senses are involve…
Genome-scale sequence data have become increasingly available in the phylogenetic studies for understanding the evolutionary histories of species. However, it is challenging to develop probabilistic models to account for heterogeneity of phylogenomic data. The multispecies coalescent model describes gene trees as independent random variables generated from a coalescence process occurring alo…
Alpha‐amylases play essential roles in germination, and the malting and brewing processes, by hydrolyzing starch granules present in the endosperm of barley. Hordeum spontaneum C. Koch, the progenitor of cultivated barley that harbors rich genetic diversity, was collected from seven different environments. To investigate the influence of microclimatic ecological divergence on a‐amylase, s…
As the field of ancient DNA (aDNA) enters its third decade, it is perhaps time to reflect on the amazing transformation that it has undergone. Early analyses of aDNA focused on mitochondrial and/or chloroplast DNA, which were abundantly available in the cell, making retrieval and reproducibility much easier. Study of mitochondrial DNA through time allows evolutionary relationships between sp…
An important model of a conserved gene cluster is called the gene team model, in which a chromosome is defined to be a permutation of distinct genes and a gene team is defined to be a set of genes that appear in two or more species, with the distance between adjacent genes in the team for each chromosome always no more than a certain threshold d. A gene team tree is a succinct way to represent …
Abstract—Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, including gene mutation, epigenetic changes in gene promoters, verexpression, and gene amplifications or deletions. We demonstrate a novel approach that identifies p…
To reveal the role of climate oscillations of the Quaternary in forming the contemporary plant diversity in the temperate Sino-Japanese Floristic Region of mainland China, we assess the phylogeographical patterns of four Sagittaria species in the region using sequence data from plastid DNA non-coding regions (psbA-trnH, the rpl16 intron and trnC-ycf6) and the internal transcribed spacers of …
In free-living animals, it has been well demonstrated that the intensity of the adrenocortical response to acute restraint stress can vary with reproductive investment during breeding. The parental care hypothesis posits that the stress response is negatively correlated with parental investment in avian species. To further test this hypothesis, we examined changes in both free and total cortico…