Sympatric speciation: a simulation model

A model of mating and population growth dependent on competition that suggests circumstances under which sympatric speciation might occur is described. The model is similar to one in a companion paper by Rosenzweig in that a heterozygote genotype, involving a new allele, is first selected by virtue of its ability to exploit a new niche and is then eliminated through competition. The superior competitor, which eliminates the heterozygote, is the homozygote for the new allele. For this process to occur the heterozygote must be sufficiently fit to exploit and invade a new niche, but not so fit that a classical polymorphism results from heterozygous advantage. This process of speciation is most likely to occur when there are vacant niches. When and where these might occur are discussed.     

Sympatric speciation: compliance with phenotype diversification from a single genotype

A novel mechanism for sympatric speciation that takes into account complex bioprocesses within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated physiological states and may coexist 'symbiotically' through appropriate mutual interaction. With mutations, the phenotypically differentiated organisms gradually come to possess distinct genotypes while maintaining their symbiotic relationship. This symbiotic speciation is robust against sexual recombination, because offspring of mixed parentage with intermediate genotypes are less fit than their parents. This leads to sterility of the hybrid. Accordingly, a basis for mating preference also arises.     

Sympatric speciation in animals: the ugly duckling grows up

Sympatric speciation has become increasingly accepted in the past decade, as a result of new models substantiating its plausibility and new evidence that the conditions specified by the models are met in many natural populations. Retrospective phylogenetic and population genetic signatures of sympatric speciation have also been derived, and these are beginning to be tested. This new work has helped increase the acceptance of sympatric speciation as a plausible process, although it remains difficult to show conclusively that specific pairs of taxa have speciated through sympatric processes alone. It might be time for a re-evaluation of the geographical classification of speciation modes in favor of one based primarily on evolutionary mechanisms     

Sympatric speciation by sexual selection: a critical reevaluation

Several empirical studies put forward sexual selection as an important driving force of sympatric speciation. This idea agrees with recent models suggesting that speciation may proceed by means of divergent Fisherian runaway processes within a single population. Notwithstanding this, the models so far have not been able to demonstrate that sympatric speciation can unfold as a fully adaptive process driven by sexual selection alone. Implicitly or explicitly, most models rely on nonselective factors to initiate speciation. In fact, they do not provide a selective explanation for the considerable variation in female preferences required to trigger divergent runaway processes. We argue that such variation can arise by disruptive selection but only when selection on female preferences is frequency dependent. Adaptive speciation is therefore unattainable in traditional female choice models, which assume selection on female preferences to be frequency independent. However, when frequency-dependent sexual selection processes act alongside mate choice, truly adaptive sympatric speciation becomes feasible. Speciation is then initiated independently of nonadaptive processes and does not suffer from the theoretical weaknesses associated with the current Fisherian runaway model of speciation. However, adaptive speciation requires the simultaneous action of multiple mechanisms, and therefore it occurs under conditions far more restrictive than earlier models of sympatric speciation by sexual selection appear to suggest.     

Protein dynamics and enzyme catalysis: insights from simulations

The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.     

Colonial breeding and speciation in birds

Summary It was recently suggested that bird species which breed colonially might be under stronger sexual selection, have faster rates of evolution and might therefore speciate more rapidly than bird species which do not. If true, then colonial taxa should contain more species than non-colonial taxa, other things being equal. When similarity through common descent is accounted for, there is little evidence for an association between the number of species in a clade and whether it is colonial or not.     

Epigenetics and phenotypic variability: some interesting insights from birds

Little is known about epigenetic mechanisms in birds with the exception of the phenomenon of dosage compensation of sex chromosomes, although such mechanisms could be involved in the phenotypic variability of birds, as in several livestock species. This paper reviews the literature on epigenetic mechanisms that could contribute significantly to trait variability in birds, and compares the results to the existing knowledge of epigenetic mechanisms in mammals. The main issues addressed in this paper are: (1) Does genomic imprinting exist in birds? (2) How does the embryonic environment influence the adult phenotype in avian species? (3) Does the embryonic environment have an impact on phenotypic variability across several successive generations? The potential for epigenetic studies to improve the performance of individual animals through the implementation of limited changes in breeding conditions or the addition of new parameters in selection models is still an open question.     

轮虫同域性物种形成:来自萼花臂尾轮虫克隆间的分子系统发育关系和生殖隔离的证据

对采自芜湖市三个不同水体中的萼花臂尾轮虫(Brachionus calyciflorus)17个克隆的线粒体COⅠ基因和rDNAITS1序列进行的分析结果表明:萼花臂尾轮虫不同克隆间COⅠ基因序列差异百分比为0-14.0%,平均为5.1%;ITS1序列差异百分比为0-7.4%,平均为2.2%。基于COⅠ基因序列构建的分子系统树(NJ树、MP树、ML树和贝叶斯树)均支持将17个克隆划分为三个姐妹种,各姐妹种间的序列差异百分比为7.2%-14.0%。基于ITS1序列构建的同样四种分子系统树也支持将17个克隆划分为三个姐妹种,但其中的克隆HE5在姐妹种中的归属与基于COⅠ基因序列构建的分子系统树所得出的结果不同,各姐妹种间的序列差异百分比为1.9%-7.4%。混交雌体和雄体间的交配实验结果表明,轮虫各姐妹种间存在着明显的生殖隔离,克隆HE5在姐妹种中的归属应与基于COⅠ基因序列构建的分子系统树所得出的结果一致;ITS1序列进化速率较低,不宜用于轮虫姐妹种的准确甄别。COⅠ基因进化钟计算结果显示,三个姐妹种间,克隆LE9所属的姐妹种早在8百万年前便分化形成出来,HE1、HE2、HE4-7所属的姐妹种于5百万年前分化产生。     

Sympatric speciation in a genus of marine reef fishes

Sympatric speciation has been contentious since its inception, yet is increasingly recognized as important based on accumulating theoretical and empirical support. Here, we present a compelling case of sympatric speciation in a taxon of marine reef fishes using a comparative and mechanistic approach. Hexagrammos otakii and H. agrammus occur in sympatry throughout their ranges. Molecular sequence data from six loci, with complete sampling of the genus, support monophyly of these sister species. Although hybridization occurrs frequently with an allopatric congener in an area of slight distributional overlap, we found no F₁ hybrids between the focal sympatric taxa throughout their coextensive ranges. We present genetic evidence for complete reproductive isolation based on SNP analysis of 382 individuals indicating fixed polymorphisms, with no shared haplotypes or genotypes, between sympatric species. To address questions of speciation, we take a mechanistic approach and directly compare aspects of reproductive isolation between allopatric and sympatric taxa both in nature and in the laboratory. We conclude that the buildup of reproductive isolation is strikingly different in sympatric vs. allopatric taxa, consistent with theoretical predictions. Lab reared hybrids from allopatric species crosses exhibit severe fitness effects in the F₁ or backcross generation. No intrinsic fitness effects are observed in F₁ hybrids from sympatric species pairs, however these treatments exhibited reduced fertilization success and complete pre‐mating isolation is implied in nature because F₁ hybrid adults do not occur. Our study addresses limitations of previous studies and supports new criteria for inferring sympatric speciation.     

Recent advances in behavioral neuroendocrinology: insights from studies on birds

Ever since investigations in the field of behavioral endocrinology were hatched with experiments on roosters, birds have provided original insights into issues of fundamental importance for all vertebrate groups. Here we focus on more recent advances that continue this tradition, including (1) environmental regulation of neuroendocrine and behavioral systems, (2) steroidogenic enzyme functions that are related to intracrine processes and de novo production of neurosteroids, and (3) hormonal regulation of neuroplasticity. We also review recent findings on the anatomical and functional organization of steroid-sensitive circuits in the basal forebrain and midbrain. A burgeoning body of data now demonstrates that these circuits comprise an evolutionarily conserved network, thus numerous novel insights obtained from birds can be used (in a relatively straightforward manner) to generate predictions for other taxa as well. We close by using birdsong as an example that links these areas together, thereby highlighting the exceptional opportunities that birds offer for integrative studies of behavioral neuroendocrinology and behavioral biology in general.     

Sympatric speciation and extinction driven by environment dependent sexual selection

A theoretical model is studied to investigate the possibility of sympatric speciation driven by sexual selection and ecological diversification. In particular we focus on the rock-dwelling haplochromine cichlid species in Lake Victoria. The high speciation rate in these cichlids has been explained by their apparent ability to specialize rapidly to a large diversity of feeding niches. Seehausen and colleagues however, demonstrated the importance of sexual selection in maintaining reproductive barriers between species. Our individual-orientated model integrates both niche differentiation and a Fisherian runaway process, which is limited by visibility constraints. The model shows rapid sympatric speciation or extinction of species, depending on the strength of sexual selection.     

Ions and blockers in potassium channels: insights from free energy simulations

Potassium ion channels enable efficient and selective permeation of K+ ions across nonpolar biological membranes. Here we review the results of recent free energy calculations related to the permeation of monovalent cations through K+ channels and to the channel inhibition by blocker compounds. In particular, the progress in computational studies of the bacterial KcsA channel is discussed.     

Ice sheets promote speciation in boreal birds

The premise that Pleistocene ice ages played an important role in generating present-day species diversity has been challenged by genetic data indicating that most of the youngest terrestrial species on Earth coalesced long before major glacial advances. However, study has been biased towards faunas distributed at low latitudes that were not directly fragmented by advancing ice sheets. Using mitochondrial sequence divergence and a molecular clock, we compared the coalescence times of pairs of avian species belonging to superspecies complexes from the high-latitude boreal forest with those of sub-boreal and tropical avifaunas of the New World. Remarkably, all coalescence events in boreal superspecies date to the Pleistocene, providing direct evidence that speciation was commonly initiated during recent glacial periods. A pattern of endemism in boreal superspecies plausibly links the timing of divergence to the fragmentation of the boreal forest by ice sheets during the Mid- and Late Pleistocene. In contrast to the boreal superspecies, only 56% of sub-boreal and 46% of tropical superspecies members coalesced during the Pleistocene, suggesting that avifaunas directly fragmented by ice sheets experienced rapid rates of diversification, whereas those distributed farther south were affected to a lesser extent. One explanation for the absence of pre-Pleistocene superspecies in boreal avifaunas is that strong selection pressures operated in boreal refugia, causing superspecies members to achieve ecological differentiation at an accelerated rate.     

Asymmetry in membrane responses to electric shocks: insights from bidomain simulations

Models of myocardial membrane dynamics have not been able to reproduce the experimentally observed negative bias in the asymmetry of transmembrane potential changes (DeltaVm) induced by strong electric shocks delivered during the action potential plateau. The goal of this study is to determine what membrane model modifications can bridge this gap between simulation and experiment. We conducted simulations of shocks in bidomain fibers and sheets with membrane dynamics represented by the LRd'2000 model. We found that in the fiber, the negative bias in DeltaVm asymmetry could not be reproduced by addition of electroporation only, but by further addition of hypothetical outward current, Ia, activated upon strong shock-induced depolarization. Furthermore, the experimentally observed rectangularly shaped positive DeltaVm, negative-to-positive DeltaVm ratio (asymmetry ratio) = approximately 2, electroporation occurring at the anode only, and the increase in positive DeltaVm caused by L-type Ca2+-channel blockade were reproduced in the strand only if Ia was assumed to be a part of K+ flow through the L-type Ca2+-channel. In the sheet, Ia not only contributed to the negative bias in DeltaVm asymmetry at sites polarized by physical and virtual electrodes, but also restricted positive DeltaVm. Inclusion of Ia and electroporation is thus the bridge between experiment and simulation.     

Regulation of nutrient intake in nectar-feeding birds: insights from the geometric framework

A nectar diet is simple in nutritional composition and easily digested, but may vary greatly in its proportions of sugar and water. Here, we apply the geometric framework, a modelling approach for investigating how animals balance nutrient needs in multidimensional and dynamic nutritional environments, to captive whitebellied sunbirds (Cinnyris talatala). We address the question of how these small birds (~8?g) prioritise sugar and water intake, and how dietary salt content interacts with sugar and water intake. Sunbirds kept at 20°C and provided with moderate to high sucrose concentrations (≥1?M), together with supplementary water, converge on an intake target of 2.79?g?day(-1) of sucrose and 7.72?g?day(-1) of water: equivalent to 0.85?M sucrose. When the birds are given more dilute sucrose concentrations, they defend their sugar intake by over-ingesting water, up to a ceiling of 47?g?day(-1). Sugar intake thus gets priority over water intake, but the birds have a finite capacity to over-ingest water to gain the target level of sugar. Regulation appears to be less precise when birds are given a choice between two sucrose solutions than when they choose between a sugar solution and supplementary water. Intake targets vary in response to internal and external factors, and sunbirds increase their sugar intake in response to increased activity and cold, irrespective of nectar concentration. They also compensate for interruptions in foraging activity, whether overnight or during the day. Interactive effects become evident when sodium is included as a third nutrient: on very dilute nectar (≤0.1?M), where sunbirds lose body mass, the addition of sodium to the diet helps to achieve the carbohydrate intake target, while raising the ceiling on water intake. This analysis provides a new perspective on nectarivory, while adding to the comparative database on nutrient regulation and emphasising water as a nutrient.     

Trophic partitioning in tropical rain forest birds: insights from stable isotope analysis

Bird communities reach their highest taxonomic and trophic diversity in tropical rain forest, but the use of different foraging strategies to meet food requirements in such competitive environments is poorly understood. Conventional dietary analyses are poorly suited to investigate dietary patterns in complex systems. We used stable carbon (¹³C/¹²C) and nitrogen (¹⁵N/¹⁴N) isotope analysis of whole blood to examine avian trophic patterns and sources of diet in the tropical rain forest of Los Tuxtlas, Veracruz, Mexico. We used stable nitrogen isotope analysis to delineate trophic levels, and stable carbon isotope analysis to distinguish the relative contribution of C-3 and CAM/C-4 ultimate sources of proteins to diets. There was large inter- and intraspecific variation in whole blood ¹³C and ¹⁵N values in 23 species of birds. Stable nitrogen isotope analysis separated birds into several trophic levels, including species that obtained their dietary protein mostly from plants, insects or a combination of both food sources. Stable carbon isotope analysis showed that most birds fed on C3-based foods but Stub-tailed Spadebills (Platyrinchus cancrominus) included C-3- and C-4/CAM-specialist individuals. Our analyses provided insights into the nutritional contribution of plant and animal sources of protein and distinguish their photosynthetic origin over relatively long average time periods.     

The mechanics of heterotypic cell aggregates: insights from computer simulations

Finite element-based computer simulations are used to investigate a number of phenomena, including tissue engulfment, cell sorting, and checkerboard-pattern formation, exhibited by heterotypic cell aggregates. The simulations show that these phenomena can be driven by a single equivalent force, namely a surface (or interfacial) tension, that results from cytoskeletal components and cell-cell adhesions. They also reveal that tissue engulfment, cell sorting, and checkerboard-pattern formation involve several discernible mechanical features or stages. With the aid of analytical arguments, we identify the conditions necessary for each of these phenomena. These findings are consistent with previous experimental investigations and computer simulations, but pose significant challenges to current theories of cell sorting and tissue engulfment.     

Anesthetic interaction with ketosteroid isomerase: insights from molecular dynamics simulations

The nature and the sites of interactions between anesthetic halothane and homodimeric Delta5-3-ketosteroid isomerase (KSI) are characterized by flexible ligand docking and confirmed by 1H-15N NMR. The dynamics consequence of halothane interaction and the implication of the dynamic changes to KSI function are studied by multiple 5-ns molecular dynamics simulations in the presence and absence of halothane. Both docking and MD simulations show that halothane prefer the amphiphilic dimeric interface to the hydrophobic active site of KSI. Halothane occupancy at the dimer interface disrupted the intersubunit hydrogen bonding formed either directly through side chains of polar residues or indirectly through the mediation of the interfacial water molecules. Moreover, in the presence of halothane, the exchange rate of the bound waters with bulk water was increased. Halothane perturbation to the dimer interface affected the overall flexibility of the active site. This action is likely to contribute to the halothane-induced reduction of the KSI activity. The allosteric halothane modulation of the dynamics-function relationship of KSI without direct competition at the enzymatic active sites may be generalized to offer a unifying explanation of anesthetic action on a diverse range of multidomain neuronal proteins that are potentially relevant to clinical general anesthesia.