Back to the future: natural history and the way forward in modern fungal ecology

The growing power and increasing availability of molecular tools for identifying fungi in environmental samples has revolutionized the way that fungal ecologists work. As a result, more people from around the globe have jumped into the fungal community sequencing endeavor. Paradoxically, as these extensive datasets accumulate we are often at a loss for interpretation due to the lack of basic autecology and natural history information for most fungi. As a result we are in danger of learning less and about more and more. I suggest that one way forward in fungal ecology is through a modern version of fungal natural history, with a focus on holistic understanding of individual species and ecosystems, but driven by modern genomic and molecular tools. By combining the extensive data generated through environmental sequencing with an intensive, molecular-based natural history we can create a synergy that will propel fungal ecology forward.     

A History of Dogs in the Early Americas

. History of Dogs in the Early Americas. Marion Schwartz. New Haven, CT: Yale University Press, 1997. 233 pp.     

Time and natural history: the changing face

There is a considerable body of knowledge on the changing structures of the craniofacial complex in the anthropology literature, which dates back to the late 19th century. This awareness of change in phenotype has not been emphasized in dysmorphology and incorporated into syndrome diagnosis until recently. In contrast to the anthropological data, where serial craniofacial measurements document different rates of growth in the individual structures of the craniofacial complex, awareness of the evolution of phenotype, in dysmorphology, has been based on an appreciation of a changing gestalt. This work has been carried out principally in Noonan syndrome. Noonan syndrome is a cardiofacial syndrome in which affected individuals may be short and mildly mentally retarded. In this autosomal dominant disorder, a marked change of phenotype with age from the newborn period, infancy, childhood, adolescence, and adulthood has been documented. Similar variation with age is likely to be found in many other dysmorphic syndromes. Increasing insight into the evolution of phenotypes should markedly increase the potential for diagnosis.     

Reviewing the history of HIV-1: spread of subtype B in the Americas

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950-1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion.     

Learning about human population history from ancient and modern genomes

Genome-wide data, both from SNP arrays and from complete genome sequencing, are becoming increasingly abundant and are now even available from extinct hominins. These data are providing new insights into population history; in particular, when combined with model-based analytical approaches, genome-wide data allow direct testing of hypotheses about population history. For example, genome-wide data from both contemporary populations and extinct hominins strongly support a single dispersal of modern humans from Africa, followed by two archaic admixture events: one with Neanderthals somewhere outside Africa and a second with Denisovans that (so far) has only been detected in New Guinea. These new developments promise to reveal new stories about human population history, without having to resort to storytelling.     

Epidemics to eradication: the modern history of poliomyelitis

Poliomyelitis has afflicted humankind since antiquity, and for nearly a century now, we have known the causative agent, poliovirus. This pathogen is an enterovirus that in recent history has been the source of a great deal of human suffering. Although comparatively small, its genome is packed with sufficient information to make it a formidable pathogen. In the last 20 years the Global Polio Eradication Initiative has proven successful in greatly diminishing the number of cases worldwide but has encountered obstacles in its path which have made halting the transmission of wild polioviruses a practical impossibility. As we begin to realize that a change in strategy may be crucial in achieving success in this venture, it is imperative that we critically evaluate what is known about the molecular biology of this pathogen and the intricacies of its interaction with its host so that in future attempts we may better equipped to more effectively combat this important human pathogen.     

The genetic history of Cochin Jews from India

Cochin Jews form a small and unique community on the Malabar coast in southwest India. While the arrival time of any putative Jewish ancestors of the community has been speculated to have taken place as far back as biblical times (King Solomon’s era), a Jewish community in the Malabar coast has been documented only since the 9th century CE. Here, we explore the genetic history of Cochin Jews by collecting and genotyping 21 community members and combining the data with that of 707 individuals from 72 other Indian, Jewish, and Pakistani populations, together with additional individuals from worldwide populations. We applied comprehensive genome-wide analyses based on principal component analysis, F _ST, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing, allele sharing autocorrelation decay and contrasting the X chromosome with the autosomes. We find that, as reported by several previous studies, the genetics of Cochin Jews resembles that of local Indian populations. However, we also identify considerable Jewish genetic ancestry that is not present in any other Indian or Pakistani populations (with the exception of the Jewish Bene Israel, which we characterized previously). Combined, Cochin Jews have both Jewish and Indian ancestry. Specifically, we detect a significant recent Jewish gene flow into this community 13–22 generations (~470–730 years) ago, with contributions from Yemenite, Sephardi, and Middle-Eastern Jews, in accordance with historical records. Genetic analyses also point to high endogamy and a recent population bottleneck in this population, which might explain the increased prevalence of some recessive diseases in Cochin Jews.     

The oldest higher true crabs (Crustacea: Decapoda: Brachyura): insights from the Early Cretaceous of the Americas

Despite the extensive fossil record of higher crabs (Eubrachyura) from Late Cretaceous and Cenozoic rocks worldwide, their Early Cretaceous occurrences are scarce and fragmentary, obscuring our understanding of their early evolution. Until now, representatives of only two families of eubrachyuran‐like crabs were known from the Early Cretaceous: Componocancridae and Tepexicarcinidae fam. nov., both monospecific lineages from the Albian (~110–100 Ma) of North and Central America, respectively. The discovery of Telamonocarcinus antiquus sp. nov. (Telamonocarcinidae) from the early Albian of Colombia, South America (~110 Ma), increases to three the number of known Early Cretaceous eubrachyuran‐like families. The ages and geographical distributions of the oldest eubrachyuran‐like taxa (i.e. Componocancridae, Telamonocarcinidae and Tepexicarcinidae fam. nov.) suggest that the oldest higher true crabs might have originated in the Americas; that they were already morphologically diverse by the late Early Cretaceous; and that their most recent common ancestor must be rooted in the Early Cretaceous, or even the Late Jurassic.     

Early Eocene Primates from Gujarat, India

The oldest euprimates known from India come from the Early Eocene Cambay Formation at Vastan Mine in Gujarat. An Ypresian (early Cuisian) age of ∼53 Ma (based on foraminifera) indicates that these primates were roughly contemporary with, or perhaps predated, the India-Asia collision. Here we present new euprimate fossils from Vastan Mine, including teeth, jaws, and referred postcrania of the adapoids Marcgodinotius indicus and Asiadapis cambayensis. They are placed in the new subfamily Asiadapinae (family Notharctidae), which is most similar to primitive European Cercamoniinae such as Donrussellia and Protoadapis. Asiadapines were small primates in the size range of extant smaller bushbabies. Despite their generally very plesiomorphic morphology, asiadapines also share a few derived dental traits with sivaladapids, suggesting a possible relationship to these endemic Asian adapoids. In addition to the adapoids, a new species of the omomyid Vastanomys is described. Euprimate postcrania described include humeri, radii, femora, calcanei, and tali, most of which show typical notharctid features and are probably attributable to asiadapines. Anatomical features of the limb elements indicate that they represent active arboreal quadrupedal primates. At least one calcaneus is proximally shorter and distally longer than the others, resembling eosimiids in this regard, a relationship that, if confirmed, would also suggest an Asian or southeast Asian faunal connection. Isolated teeth from Vastan Mine recently attributed to a new eosimiid, Anthrasimias gujaratensis, appear to provide that confirmation. However, their attribution to Eosimiidae is equivocal. They are similar to teeth here tentatively referred to Marcgodinotius, hence A. gujaratensis may be a junior synonym of M. indicus. Corroboration of eosimiids at Vastan requires more compelling evidence. Although definitive conclusions are premature, available evidence suggests that the Vastan adapoids, at least, were derived from western European stock that reached India near the Paleocene-Eocene boundary.     

Cephalopod chromatophores: neurobiology and natural history

The chromatophores of cephalopods differ fundamentally from those of other animals: they are neuromuscular organs rather than cells and are not controlled hormonally. They constitute a unique motor system that operates upon the environment without applying any force to it. Each chromatophore organ comprises an elastic sacculus containing pigment, to which is attached a set of obliquely striated radial muscles, each with its nerves and glia. When excited the muscles contract, expanding the chromatophore; when they relax, energy stored in the elastic sacculus retracts it. The physiology and pharmacology of the chromatophore nerves and muscles of loliginid squids are discussed in detail. Attention is drawn to the multiple innervation of dorsal mantle chromatophores, of crucial importance in pattern generation. The size and density of the chromatophores varies according to habit and lifestyle. Differently coloured chromatophores are distributed precisely with respect to each other, and to reflecting structures beneath them. Some of the rules for establishing this exact arrangement have been elucidated by ontogenetic studies. The chromatophores are not innervated uniformly: specific nerve fibres innervate groups of chromatophores within the fixed, morphological array, producing 'physiological units' expressed as visible 'chromatomotor fields'. The chromatophores are controlled by a set of lobes in the brain organized hierarchically. At the highest level, the optic lobes, acting largely on visual information, select specific motor programmes (i.e. body patterns); at the lowest level, motoneurons in the chromatophore lobes execute the programmes, their activity or inactivity producing the patterning seen in the skin. In Octopus vulgaris there are over half a million neurons in the chromatophore lobes, and receptors for all the classical neurotransmitters are present, different transmitters being used to activate (or inhibit) the different colour classes of chromatophore motoneurons. A detailed understanding of the way in which the brain controls body patterning still eludes us: the entire system apparently operates without feedback, visual or proprioceptive. The gross appearance of a cephalopod is termed its body pattern. This comprises a number of components, made up of several units, which in turn contains many elements: the chromatophores themselves and also reflecting cells and skin muscles. Neural control of the chromatophores enables a cephalopod to change its appearance almost instantaneously, a key feature in some escape behaviours and during agonistic signalling. Equally important, it also enables them to generate the discrete patterns so essential for camouflage or for signalling. The primary function of the chromatophores is camouflage. They are used to match the brightness of the background and to produce components that help the animal achieve general resemblance to the substrate or break up the body's outline. Because the chromatophores are neurally controlled an individual can, at any moment, select and exhibit one particular body pattern out of many. Such rapid neural polymorphism ('polyphenism') may hinder search-image formation by predators. Another function of the chromatophores is communication. Intraspecific signalling is well documented in several inshore species, and interspecific signalling, using ancient, highly conserved patterns, is also widespread. Neurally controlled chromatophores lend themselves supremely well to communication, allowing rapid, finely graded and bilateral signalling.     

Puddling: from natural history to understanding how it affects fitness

The term ‘puddling’ includes feeding on (dried) mud and various excrements and secretions of vertebrates, and carrion. It is thought to be a form of supplementary feeding, not targeted at obtaining energy. Although the natural history of the puddling phenomenon in herbivorous arthropods becomes better known, it is still largely unclear how puddling (in particular for sodium) affects fitness despite the growing knowledge of insect physiology at the cellular level. If we follow the definition used for puddling in Lepidoptera, representatives of a wide range of herbivorous and detrivorous terrestrial arthropods (Lepidoptera, Orthoptera, Blattodea, Hymenoptera, Hemiptera, Diptera, and Diplopoda) have been observed to puddle. It appears that those species with diets low in sodium (e.g., folivorous larvae) puddle for sodium whereas those with diets low in nitrogen (e.g., detritivores) puddle for nitrogen. Sex differentials in puddling behavior can usually be explained by transfers of nutrients from males to females during mating. Puddling is rare or absent in immature stages and there is some evidence that nutrients from puddles increase female reproductive success. Strong evidence for the widely cited hypothesis that sodium from puddles is used to enhance neuromuscular activity is still lacking. High mobility and long life spans could be associated with puddling behavior, whereas insects that are concealed or well defended are less likely to puddle (e.g., beetles). The role that risks of pathogen and parasite infection as well as predation at puddling substrates may play in the evolution of puddling remains virtually unexplored.     

Early Permian brachiopod faunas from Peninsular India: Their Gondwanan relationships

The Early Permian (Late Asselian? to Aktastinian?) brachiopod faunas of Peninsular India are revised in terms of current taxonomy. Genera such as Semilingula, Arctitreta, Etherilosia, Strophalosia, Aulosteges, Bandoproductus, Cyrtella, Neospirifer, Crassispirifer, Tomiopsis and Gilledia confirm the Gondwanan aspect of the faunas and a close relationship, at the generic level, to the Early Permian brachiopod faunas of Western Australia. Peninsular Indian Early Permian brachiopod faunas belong to a complex of Gondwanan and peri‐Gondwanan faunas from Oman and the Pamirs in the West to Australasia in the east. This distribution implies relative freedom of migration for the faunas along the northern margin of Gondwana during the Early Permian.     

African bees in the Americas: Insights from biogeography and genetics

The spread of African honey bees in South and Central America is one of the most remarkable and certainly among the most highly publicized instances of biological invasion. Their aggressive nest defense has led to numerous stinging incidents and even deaths; aggressiveness, coupled with a tendency to abandon the nest when disturbed, has also caused serious disruption of beekeeping and pollination industries in regions that they have invaded. The rapid spread of African bees in the Americas and their recent arrival in the United States have sparked interest in development of genetic tools for identification of honeybee populations. This in turn has renewed interest in honeybee biogeography.     

Divide and conquer: understanding the natural history of cancer

XVth Meeting of the European Association for Cancer Research: five natural histories of human cancerStockholm, Sweden, 15–19 August 1998     

Genomic creativity and natural selection: a modern synthesis

In the early 1930s, the synthesis of Darwinian natural selection, mutation, and Mendelian genetics gave rise to the paradigm of 'modern Darwinism', also known as 'neo-Darwinism'. This has contributed greatly to our understanding. But increasing knowledge of other mechanisms, including endosymbiosis, genetic and genomic duplication, polyploidy, hybridization, epigenetics, horizontal gene transfer in prokaryotes, and the modern synthesis of embryonic development and evolution, has widened our horizons to a diversity of possibilities for change. All of these can be gathered under the umbrella concept of 'genomic creativity', which, in partnership with natural selection, affords a more comprehensive modern explanation of evolution.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 655–672.     

Contributions to the rotifer fauna of ORISSA,India

This paper deals with 36 species of monogonont rotifers (belonging to 10 eurotatorien families) collected from Sambalpur (Orissa State) in Eastern India. Of the reported taxa, 15 species have been added as new records to the previous list from this region while one species represents a new record from this country.