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…
The closely related Camponotus renggeri and Camponotus rufipes (subgenus Myrmothrix) often live in sympatry in the Brazilian ‘cerrado’ savannah, and are distinguished by nuances in their blackish body colour and by the colour of the legs. Variation in morphological characters, however, makes species separation difficult and it has been suggested that the two species should be merged into…
The Permian and Triassic were key time intervals in the history of life on Earth. Both periods are marked by a series of biotic crises including the most catastrophic of such events, the end-Permian mass extinction, which eventually led to a major turnover from typical Palaeozoic faunas and floras to those that are emblematic for the Mesozoic and Cenozoic. Here we review patterns in Permian–T…
Neodryinus typhlocybae (Hymenoptera:Dryinidae) is a natural enemy of the planthopper Metcalfa pruinosa, which was introduced from North America into Europe and has become established in various regions as a pest species. Vibrational signals play a crucial role in the communication of M. pruinosa, which appears to be exploited by N. typhlocybae. Scanning and transmission electron microscopy have…
Arable weeds are one of the most endangered species groups in Europe. Modern agriculture and intensive land-use management are the main causes of their dramatic decline. However, besides the changes in land use, climate change may further challenge the adaptability of arable weeds. Therefore, we investigated the response pattern of arable weeds to different water potential and temperature regim…
1. Statistical approaches for testing hypotheses of heterogeneity in fitness functions are needed to accommodate studies of phenotypic selection with repeated sampling across study units, populations or years. In this study, we tested directly for among-population variation in complex fitness functions and demonstrate a new approach for locating the region of the trait distribution where var…
Mediterranean-type streams are characterized by great seasonal and annual variation in flow. We studied the biology of the freshwater mussel Unio tumidiformis in such a stream, the Vasc~ao River in southern Portugal, during a period of great interannual variation in hydrology. We studied growth patterns of the mussels between 2002–2008, and the reproductive cycle between 2005–2006. Life-his…
Rising atmospheric CO2 concentrations (e[CO2]) are presumed to have a significant impact on plant growth and yield and also on mineral nutrient composition, and therefore, on nutritional quality of crops and vegetables. To assess the relevance of these effects in future agroecosystems it is important to understand how e[CO2] interacts with other environmental factors. In the present study, we e…
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…
In recent years, the Intermountain West (IM West), consisting of the mountains, basins, and plateaus lying between the Cascade Range and the Sierra Nevada on the west and the Rocky Mountains on the east, has changed dramatically. What was once a vast open area with barely enough population to qualify for statehood is still open and vast, but sparse settlements have metastasized into cities …
Yet another cell and molecular biology book? At the very least, you would think that if I was going to write a textbook, I should write one in an area that really needs one instead of a subject that already has multiple excellent and definitive books. So, why write this book, then? First, it’s a course that I have enjoyed teaching for many years, so I am very familiar with what a student …
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…