The role of genetic biases in shaping the correlations between languages and genes

It has recently been proposed [Dediu, D., Ladd, D.R., 2007. Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin. Proc. Natl Acad. Sci. USA 104(26), 10944-10949] that genetically coded linguistic biases can influence the trajectory of language change. However, the nature of such biases and the conditions under which they can become manifest have remained vague. The present paper explores computationally two plausible types of linguistic acquisition biases in a population of agents implementing realistic genetic, linguistic and demographic processes. One type of bias represents an innate asymmetric initial state (initial expectation bias) while the other an innate asymmetric facility of acquisition (rate of learning bias). It was found that only the second type of bias produces detectable effects on language through cultural transmission across generations and that such effects are produced even by weak biases present at low frequencies in the population. This suggests that learning preference asymmetries, very small at the individual level and not very frequent at the population level, can bias the trajectory of language change through the process of cultural transmission.     

A statistical test of hypotheses on the organization and origin of the genetic code

Summary Theories of the origin of the genetic code assign different weights to amino acid properties such as polarity and precursor-product relationship. Previous statistical work on the origin of the genetic code has produced controversial results. We analyze relationships between various amino acid and tRNA properties by one and the same statistical method. It is shown that polarities as well as precursor-product relationships are both likely to have been important in shaping the genetic code, together with codon swapping that left protein sequences intact.     

Identification of essentially derived varieties with molecular markers: an approach based on statistical test theory and computer simulations

Genetic similarities (GS) based on molecular markers have been proposed as a tool for identification of essentially derived varieties (EDVs). Nevertheless, scientifically reliable criteria for discrimination of EDVs and independently derived varieties with GS estimates are scanty, and implementation into practical breeding has not yet taken place. Our objectives were to (1) assess the influence of chromosome number and length, marker density, and distribution, as well as the degree of polymorphism between the parental inbreds on the distribution of GS between parental inbreds and their progenies [GS(P1,O)] derived from F2 and different backcross populations and (2) evaluate these factors with regard to the power for distinguishing F2- versus BC1- and BC1- versus BC2-derived lines with molecular markers. We developed an approach based on statistical test theory for the identification of EDVs with molecular markers. Standard deviations and overlaps of distributions of GS(P1,O) of F2-, BC1-, and BC2-derived lines were smaller with (1) increasing chromosome number and length, (2) increasing marker density, and (3) uniformly instead of randomly distributed markers, approaching a lower boundary determined by the genetic parameters. The degree of polymorphism between the parental inbreds influenced the power only if the remaining number of polymorphic markers was low. Furthermore, suggestions are made for (1) determining the number of markers required to ascertain a given power and (2) EDV identification procedures.     

Clutch size and population stability in birds: A test of hypotheses

Summary The general consensus of current theoretical models for the evolution of reproductive rates is that large clutches are selected for in unstable populations. Predictions from these theories on the geographical variation in clutch size in passerine birds are tested, assuming that breeding populations, often of low density, close to the borders of their distributional ranges, are more unstable than those, of usually higher breeding densities, in more central areas. The predictions were only found to be verified for the latitudinal variation in clutch size for hole-nesting species. For the same geographical gradient (Switzerland-Finland) for the open-nesters, and for all species for the altitudinal gradient (in Switzerland), no support was found for the hypotheses and, in fact, there was a tendency for the reverse trend, viz. that mean clutch size is positively correlated with population size. For instance, those few species which did exhibit an altitudinal increase in mean clutch size, from lowland to highland, are those generally characterized from their distributional ranges as highland species.     

A simulation test bed for hypotheses of genome evolution

MOTIVATION: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution and lateral genetic transfer. Simulation tools are essential for both the generation of data under different evolutionary models and the validation of analytical methods on such data. However, meaningful investigation of phenomena such as lateral genetic transfer requires the simultaneous consideration of many underlying evolutionary processes. RESULTS: We have developed EvolSimulator, a software package that combines non-stationary sequence and gene family evolution together with models of lateral genetic transfer, within a customizable birth-death model of speciation and extinction. Here, we examine simulated data sets generated with EvolSimulator using existing statistical techniques from the evolutionary literature, showing in detail each component of the simulation strategy. AVAILABILITY: Source code, manual and other information are freely available at www.bioinformatics.org.au/evolsim. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Genetic variation within two linguistic Amerindian groups: relationship to geography and population size

Nine Carib and eight Tupi groups were studied for a minimum of eight common polymorphic systems and compared in terms of genetic distances using the methods of Nei and Edwards. Two levels of genetic information were distinguished, one with a maximum of 20 loci and another with a maximum of 12 loci considered. The dendrograms produced consistent, reproducible results, independent of the method used, when a minimum of ten polymorphic systems were included in the analysis. Irrespective of the number of systems or the method used, the Tupi showed two to three times higher average interpopulation genetic distances than the Carib groups, which may be due to their lower average population sizes, allowing for the action of genetic drift and/or founder effects, as these two sets of populations do not differ significantly in geographic range, years of contact with non-Indians, or degree of acculturation.     

五条河流青海湖裸鲤的同工酶变异

为全面了解青海湖裸鲤遗传多样性现状,采用水平淀粉凝胶电泳技术分析了青海湖裸鲤[样品采自青海湖的五条支流,分别为泉吉河(QJ)、沙柳河(SL)、哈尔盖河(HEG)、布哈河(BH)以及甘子河(GZ)]的13种同工酶,共记录26个位点,统计了基因频率,计算了其遗传多样性。结果表明:26个基因位点中多态位点6个,分别为Pgm、Hk、Cat、Gdh、Es-t1、S-Mdh,多态位点比例(P0.99)为23.08%,表明青海湖裸鲤的五个群体皆具有较高的遗传多样性水平;分别计算了五个群体的平均杂合度(H)为0.1161(HEG)、0.1178(GZ)、0.1304(SL)、0.1305(BH)、0.1287(QJ),多态位点比例(Ae)分别为1.3112(BH)、1.3069(SL)、1.2542(GZ)、1.2492(HEG)、1.2453(QJ);除泉吉河群体外,其它四个群体的遗传偏离指数均为负数,表明多数群体处于一定程度的杂合子缺失状态;计算了五个群体间的遗传距离以及遗传相似度,结果显示群体间遗传距离与遗传相似度与各个河流的地理位置具有很强的相关性;根据五个群体的遗传距离进行了聚类分析,通过构建系统树图将其基本分为两大种群,甘子河与哈尔盖河两群体为一类群,另外三个群体分为一个类群;计算群体间的基因流(Nm)为7.2013,说明河道之间具有较为广泛的基因交流,并计算了两两群体间的基因流,其中布哈河群体与其它群体间的基因交流都较为广泛。     

A simulation test of Smith's “degrees of freedom” correction for comparative studies

Computer simulation was used to test Smith's (1994) correction for phylogenetic nonindependence in comparative studies. Smith's method finds effective N, which is computed using nested analysis of variance, and uses this value in place of observed N as the baseline degrees of freedom (df) for calculating statistical significance levels. If Smith's formula finds the correct df, distributions of computer-generated statistics from simulations with observed N nonindependent species should match theoretical distributions (from statistical tables) with the df based on effective N. The computer program developed to test Smith's method simulates character evolution down user-specified phylogenies. Parameters were systematically varied to discover their effects on Smith's method. In simulations in which the phylogeny and taxonomy were identical (tests of narrow-sense validity), Smith's method always gave conservative statistical results when the taxonomy had fewer than five levels. This conservative departure gave way to a liberal deviation in type I error rates in simulations using more than five taxonomic levels, except when species values were nearly independent. Reducing the number of taxonomic levels used in the analysis, and thereby eliminating available information regarding evolutionary relationships, also increased type I error rates (broad-sense validity), indicating that this may be inappropriate under conditions shown to have high type I error rates. However, the use of taxonomic categories over more accurate phylogenies did not create a liberal bias in all cases in the analysis performed here. The effect of correlated trait evolution was ambiguous but, relative to other parameters, negligible. © 1995 Wiley-Liss, Inc.     

A reaction diffusion model of C-N-S-O species in some arctic sediments

Abstract A reaction diffusion model was used to simulate the mineralization processes in an Arctic sediment. The simulation and the actual sediment were compared in relation to profiles of O₂, NO₃ and NH₄⁺. The site of particulate organic matter (POM) degradation was the single most important factor in fitting the simulation profiles to those of the sediment. It was deduced that most POM degradation occurred close to the sediment surface. When a reasonably good simulation had been obtained, the sensitivity of the model to changes in other parameters was investigated. Increases in POM degradation in the upper sediment resulted in increases in concentration of NH₄⁺ and NO₃⁻, but further increases in POM degradation created anoxic conditions below 3 mm, resulting in decreases in NO₃⁻ concentrations. The model was relatively intensive to changes in POM degradation in the lower sediment layers; increases led to more anoxic conditions and to less NO₃⁻. Increases in the C/N ratio of the POM in the lower sediment layers had little effect; increases in C/N in the upper layers led to a decrease in NH₄⁺ and NO₃⁻. The model was sensitive to changes in the first order rate constant for nitrification, but not for denitrification. Decreases in the K _m for O₂ of the nitrifying bacteria had no effect on the profiles.     

Distribution and coexistence of shrews in patchy landscapes: A field test of multiple hypotheses

Despite the important role of shrews (Soricomorpha: Soricidae) in the functioning of ecosystems, as predators and prey, the effects of habitat loss and fragmentation on this guild of mammals are still unclear. We studied the distribution of 5 species (the greater white toothed shrew Crocidura leucodon; the lesser white toothed shrew Crocidura suaveolens; the pigmy shrew Sorex minutus; the Appennine shrew Sorex samniticus and the Etruscan shrew Suncus etruscus) in a fragmented landscape in central Italy.Shrews were trapped with pitfall traps made from plastic water bottles, the number of traps increased with patch size. A total of 170 individuals, of 5 species of shrews were captured. Shrews were widely distributed in our study area, however patch occupancy was determined mainly by vegetation and geometrical characteristics of the patches. Our data supports the hypotheses that patterns of habitat selection and the dynamics of seasonal abundance (habitat and temporal partitioning between similarly sized species) reduce competitive pressure, thus allowing coexistence of shrews in relatively species-rich assemblages, for such small amounts of habitat. The most important outcome of our results is the crucial role played by vegetation structure in determining distribution patterns. These results strongly suggest that measurements of the vegetation structure of habitat patches should always be included as explanatory variables when studying the distribution of shrews in fragmented landscapes.     

Evolve III: A discrete events model of an evolutionary ecosystem

Evolve III is a discrete events model of an evolutionary ecosystem. The model includes three levels of organization: population, organism and genetic structure. Each of these components was modeled independently, so that selective replacement of subsystems can be used to create families of models capable of testing alternative hypotheses about the real system. To demonstrate the use of the model we describe an experiment on the relationship between adaptability of populations and the variability of the environment. Populations cultured in a constant environment usually dominated those cultured in a variable environment when both were placed in a variable environment at an early stage of development, whereas the opposite is the case at later stages of development. This agrees with experiments on laboratory microcosms and lends credence to the potential predictive value of the model.     

The origins of lactation and the evolution of milk: a review with new hypotheses

Lactation is central to mammalian reproduction, and an understanding of the origins of lactation is necessary to comprehend the early evolution of the Class Mammalia. In modern mammals, lactation is a staggeringly complex phenomenon involving morphological, physiological, biochemical, ecological, and behavioural adaptations. Because such a complex web of adaptations could not have arisen de novo, lactation must have begun as a much simpler process. Hypotheses regarding the original adaptive value of proto-lacteal secretions invoke thermoregulatory, antibiotic, behavioural or nutritive functions. In this review, we evaluate each of these hypotheses and attempt to reconstruct the origins of lactation in the light of current concepts of the biology of early mammals and their ancestors, the origin of mammary glands, the evolution of extravitelline nutrient provision, and the physiology and biochemistry of milk synthesis and secretion. Drawing upon empirical evidence and theoretical considerations, we present a gradualistic scenario involving the following steps. First, incubation of eggs was aided by development of a vascularized abdominal incubation patch. Secondly, anti-microbial secretions from cutaneous glands of the incubation patch enhanced survival of eggs or offspring. At this stage, these secretions could have supplemented vitelline nutrients (in much the same way as oviductal secretions do in monotremes), perhaps facultatively. Subsequently, hypertrophy and specialization of cutaneous glands accompanied the controlled production of a copious, nutritious secretion, which eventually evolved into a primary source of energy for development and growth of the offspring. We outline important events in the evolution of milk, and suggest studies likely to provide indirect tests of the evolutionary hypotheses discussed.     

A test of alternative hypotheses for kin recognition in cannibalistic tiger salamanders

The function of kin recognition is controversial. We investigatedtheadaptive significance of kin discrimination in cannibalistictiger salamanderlarvae, Ambystoma tigrinum. Previous laboratoryexperiments show thatcannibals preferentially consume lessrelated individuals. We hypothesizedthat this example of kinrecognition (1) is a laboratory artifact, (2) is aby-productof sibship-specific variation in escape responses, becausecannibalsfrom families with rapid responses may be more likely to cannibalizeslowlyescaping non-kin, (3) is an epiphenomenon of species recognition,(4)functions in disease avoidance, because kin may be moreinfectious thannon-kin, or (5) is favored by kin selection.We evaluated these fivehypotheses by using laboratory and fieldexperiments to test specificpredictions made by each hypothesis.We rejected hypotheses 1-4 above because(1) kin recognitionwas expressed in the wild, (2) escape responses did notreliablypredict whether a cannibal would ingest kin or non-kin, (3)kinrecognition was not most pronounced in populations wheretiger salamandersco-occur with other species of salamanders,and (4) non-kin prey were morelikely than kin to transmit pathogensto cannibals. However, we establishedthat the necessary conditionfor kin selection, Hamilton's rule, was met.Thus, our resultsimplicate kin selection as the overriding reason thatcannibalistictiger salamanders discriminate kin.     

A test of two hypotheses explaining the seasonality of reproduction in temperate mammals

1. Two proposed hypotheses about energy allocation were tested to explain the patterns of seasonal reproduction found in temperate mammals. The two hypotheses predict either that total demand for energy is greater during reproduction than during winter (when thermoregulatory costs are high) (Increased Demand Hypothesis) or that total costs during winter are greater than or equal to total costs during reproduction (Reallocation Hypothesis).
2. Data were compiled from the literature on summer (non-reproducing) and winter metabolic rates of temperate mammals, and were used on litter sizes and a published equation to predict metabolic rates during lactation.
3. All three measures of metabolic rate scaled to body mass with slopes significantly less than one. Metabolic rates during winter averaged ≈ 2 times greater than those of non-reproducing mammals during summer. On average, predicted metabolic rates during lactation were not significantly greater than during winter, but for some individual species they clearly were.
4. It is suggested that neither the Reallocation nor the Increased Demand Hypothesis can fully explain seasonal reproductive patterns in temperate mammals.