EXTINCTION AND RECOLONIZATION: THEIR EFFECTS ON THE GENETIC DIFFERENTIATION OF LOCAL POPULATIONS

In this paper, we use a model by Slatkin (1977) to investigate the genetic effects of extinction and recolonization for a species whose population structure consists of an array of local demes with some migration among them. In particular, we consider the conditions under which extinction and recolonization might enhance or diminish gene flow and increase or decrease the rate of genetic differentiation relative to the static case with no extinctions. We explicitly take into account the age-structure that is established within the array of populations by the extinction and colonization process. We also consider two different models of the colonization process, the so-called “migrant pool” and “propagule pool” models. Our theoretical studies indicate that the genetic effects of extinction and colonization depend upon the relative magnitudes of K, the number of individuals founding new colonies, and 2Nm, twice the number of migrants moving into extant populations. We find that these genetic effects are surprisingly insensitive to the extinction rate. We conclude that, in order to assess the genetic effects of the population dynamics, we must first answer an important empirical question that is essentially ecological: is colonization a behavior distinct from migration?     

On a possible biological spectroscopy

A new type of physical transition, denotedS→S ^*, has been detected in irradiated organic molecules (λ=546 nm) through their interaction with specific biological macromolecules. In a specific enzyme-substrate interaction, a clear enhancement of the reaction rate is observed, when the substrate is irradiated with sharply well defined times. These “efficient irradiation times” are always of the 5k sec type (k=1, 2, 3, …). They have been consistently revealed in a great number of specific biological interactions. The present note demonstrates an important property, i.e. that forevery irradiation time aS→S ^* transition is induced in organic molecules. It is shown that for any irradiation times different from the 5k sec type (k=1, 2, 3, …) states of theS ^* type may occur, but the biological macromolecules may “detect” only theS ^* states induced by irradiations of the 5k sec type.     

Mechanisms of bovine liver glutamate dehydrogenase self-association. I. Kinetic evidence for a random association of polymer chains.

We have undertaken a study of the mechanism of bovine liver glutamate dehydrogenase self-association with scattered light temperature-jump and stopped-flow relaxation techniques. Our results indicate a “random association” mechanism in which association-dissociation reactions occur between all polymerized forms of the oligomer according to

where the specific rate-constants k_a and k_d are independent of chain length. At 15 °C we find k_a = 1.5 × 10⁶m⁻¹s⁻¹ and k_d = 5 s⁻¹. Standard thermodynamic functions and activation parameters have been determined from equilibrium and kinetic experiments at different temperatures. Large entropy effects and heat capacities indicate water participation in the self-aggregation process. We suggest that the rate-determining step in the association of glutamate dehydrogenase molecules is the “melting” of a layer of ordered water structure between two hydrophobic contact sites.     

How might Gyrodactylus parasitism modify trade-offs between female preference and susceptibility of males to predation in Trinidadian guppies?

A number of examples exist of trade-offs between mating success and survival; that is, success in one fitness component comes at the cost of success in the other fitness component. However, these expected trade-offs are – perhaps even more commonly – not observed. One explanation for this apparent paradox of missing trade-offs could be that the other factors generating fitness variation across individuals confound or obscure the expected trade-off. These confounding effects could arise in two general ways: (i) the additional source of variation could positively (or negatively) influence both fitness components (“shared confounder” hypothesis), or (ii) the additional source of variation could influence only one fitness component (“non-shared confounder” hypothesis). We tested whether parasitism by Gyrodactylus spp. could be a confounder of trade-offs between female preference and susceptibility to predation for male Trinidadian guppies (Poecilia reticulata). As in previous work, we did not find the expected trade-off; that is, the males preferred by females were not more likely to be eaten by predators. Because half of the experimental males were infected by Gyrodactylus in a paired design, we were able to show that females discriminated against infected males, but that infected males were not more susceptible to predation. Our results thus provide support for the non-shared confounder hypothesis. That is, by negatively affecting one fitness component (female choice) but not the other (susceptibility to predation), parasitism by Gyrodactylus could obscure the expected trade-off between female preference and susceptibility to predation.     

Selection never dominates drift (nor vice versa)

The probability that the fitter of two alleles will increase in frequency in a population goes up as the product of N (the effective population size) and s (the selection coefficient) increases. Discovering the distribution of values for this product across different alleles in different populations is a very important biological task. However, biologists often use the product Ns to define a different concept; they say that drift “dominates” selection or that drift is “stronger than” selection when Ns is much smaller than some threshold quantity (e.g., ½) and that the reverse is true when Ns is much larger than that threshold. We argue that the question of whether drift dominates selection for a single allele in a single population makes no sense. Selection and drift are causes of evolution, but there is no fact of the matter as to which cause is stronger in the evolution of any given allele.     

Population Genetics,Dispersal, and Kinship Among Wild Squirrel Monkeys (Saimiri sciureus macrodon): Preferential Association Between Closely Related Females and Its Implications for Insect Prey Capture Success

Little genetic information is available to evaluate hypotheses concerning the parameters that affect population genetic structure in primate taxa that exhibit interspecific variation in social systems, such as squirrel monkeys (Saimiri). Here, we used genetic data to assess dispersal patterns, kin structure, and preferential association with same-sex kin in a wild population of Saimiri sciureus macrodon. We also analyzed behavioral data to assess whether individuals that maintain shorter interindividual distances show increased insect foraging success. If there was greater male than female dispersal, then we expected mean pairwise relatedness, F _ST values, and intragroup mean corrected assignment indices to be greater among adult females than among adult males. We also expected matrices of pairwise affinity indices (PAIs) for “association” (time spent ≤5 m) and “proximity” (time spent ≤10 m) among female dyads to positively correlate with a matrix of female pairwise relatedness. Not only did we find support for female philopatry, but we also found significant positive relationships between the relatedness matrix and each of the PAI matrices: females were more likely to be associated with (and proximal to) close female relatives than more distant relatives or unrelated individuals. Foraging analyses revealed that females had higher insect capture rates than males, and this sex difference may be related to a smaller mean interindividual distance among closely related female group members. Our result shows how estimates of genetic relatedness are useful for testing predictions regarding the evolution of sex-biased dispersal patterns, as well as potential relationships between kin-biased social behaviors and foraging success.     

AVPR1A Variation in Chimpanzees (Pan troglodytes): Population Differences and Association with Behavioral Style

Primates and other mammals show measurable, heritable variation in behavioral traits such as gregariousness, timidity, and aggression. Connections among behavior, environment, neuroanatomy, and genetics are complex, but small genetic differences can have large effects on behavioral phenotypes. One of the best examples of a single gene with large effects on natural variation in social behavior is AVPR1A, which codes for a receptor of the peptide hormone arginine vasopressin. Work on rodents shows a likely causal association between AVPR1A regulatory polymorphisms and social behavior. Chimpanzees also show variation in the AVPR1A regulatory region, with some individuals lacking a ca. 350-bp segment corresponding to a putative functional element. Thus, chimpanzees have a “short” allele (segment deletion) and a “long” allele (no deletion) at this locus. Here we compare AVPR1A variation in two chimpanzee populations, and we examine behavioral and hormonal data in relation to AVPR1A genotypes. We genotyped AVPR1A in a captive population of western chimpanzees (Pan troglodytes verus, New Iberia Research Center; N = 64) for which we had quantitative measures of personality (based on 15 behavioral style indices, calculated from 3 yr of observational data), dominance rank, and baseline testosterone levels. We also provide the first assessment of AVPR1A genotype frequencies in a wild eastern chimpanzee population (Pan troglodytes schweinfurthii, Ngogo community, Kibale National Park, Uganda; N = 26). Our results indicated that the AVPR1A long allele was associated with a “smart” social personality in captive western chimpanzees, independent of testosterone levels. Although the frequency of the long allele was relatively low in captive western chimpanzees (0.23), it was the major allele in wild eastern chimpanzees (0.62). Our finding that allele and genotype frequencies for the AVPR1A polymorphism differ among chimpanzee populations also highlights the need for comparative studies —across subspecies and research sites— in primate behavioral genetics.     

Persistence of Common Alleles in Two Related Populations or Species

Mathematical studies are conducted on three problems that arise in molecular population genetics. (1) The time required for a particular allele to become extinct in a population under the effects of mutation, selection, and random genetic drift is studied. In the absence of selection, the mean extinction time of an allele with an initial frequency close to 1 is of the order of the reciprocal of the mutation rate when 4Nv << 1, where N is the effective population size and v is the mutation rate per generation. Advantageous mutations reduce the extinction time considerably, whereas deleterious mutations increase it tremendously even if the effect on fitness is very slight. (2) Mathematical formulae are derived for the distribution and the moments of extinction time of a particular allele from one or both of two related populations or species under the assumption of no selection. When 4Nv << 1, the mean extinction time is about half that for a single population, if the two populations are descended from a common original stock. (3) The expected number as well as the proportion of common neutral alleles shared by two related species at the tth generation after their separation are studied. It is shown that if 4Nv is small, the two species are expected to share a high proportion of common alleles even 4N generations after separation. In addition to the above mathematical studies, the implications of our results for the common alleles at protein loci in related Drosophila species and for the degeneration of unused characters in cave animals are discussed.     

States of myosin subfragment-1 studied by catalyzed ascorbate reduction of bound spin label.

The second-order rate constant, k, whereby ascorbate reduces spin label, N-(1-oxyl-2, 2,6,6-tetramethyl-4-piperidyl) iodoacetamide, bound to the fast-reacting (SH₁) thiol groups of heavy meromyosin (HMM) has been compared with the k whereby ascorbate reduces free spin label in the same solvent. It is clear that the k of protein-bound spin label is primarily determined by conditions “on-board” subfragment-1 (S-1), rather than by properties of the solvent. First, in saturating [STP] the k of HMM-bound spin label was much greater than the k of free spin label, and both k's were independent of [KCl], from 0.05 to 1 m. Second, in the absence of ATP, or even in the presence of ADP, the k of HMM-bound spin label was less than the k of free spin label at l m KCl, and much more in a 0.05 m KCl. The organized structure of S-1 is required for observing the change of k with ATP, because the change of k disappeared on denaturing HMM with either guanidine hydrochloride or urea.Measuring k can be a “probe” to specify HMM states. However, the parameter, k, is conceptually dissimilar to measuring peak heights on an EPR spectrum. Experimentally we have observed that when [KCl] is increased, while [MgATP] = 0, spectral peak height is constant, but k varies remarkably. At no [KCl] did excess F-actin affect k. Quantitative examination of metal contamination (e.g., Cu, Fe) in HMM showed that changes in the k of HMM-bound spin label cannot arise from changes in proximity to contaminating metal redox catalysts bound to HMM.An intramolecular participant in the reaction of ascorbate with bound nitroxyl half inhibits the Ca²⁺-ATPase of spin labeled HMM, so signal annihilation and ATPase activity are closely correlated in time. The rate of signal annihilation is unaffected by prior reaction of the “SH₂” thiols with N-ethylmaleimide.     

Depth-selection behavior and longevity in Daphnia: an evolutionary test for the predation-avoidance hypothesis

The classic evolutionary theory of senescence predicts that long lifespan evolves under low risk of extrinsic mortality. As lakes present planktonic animals with vertical gradients of mortality risk associated with fish predation, we expected the individual lifespan of Daphnia of the “hypolymnetic” clones to be longer than that of “epilimnetic” Daphnia. In order to test this prediction, we performed a laboratory study on 14 clones from the D. longispina species complex, taken during the daytime either from epilimnion or hypolimnion of three mesotrophic lakes. “Epilimnetic” Daphnia started reproduction earlier, aged faster, and lived shorter than their “hypolimnetic” conspecifics. Our results indirectly support the predation-avoidance hypothesis as the ultimate explanation for depth-selection behavior in Daphnia.     

Extinction and fixation times with dominance and inbreeding

The effect of partial inbreeding on extinction and fixation times of a selected allele with partial dominance is studied using a diffusion model. Asymptotic approximations are obtained for large populations and the accuracy of the approximations was found to increase with inbreeding level. They show that inbreeding reduces extinction and fixation times compared to random mating at least by a factor 1+F, where F is Wright’s fixation index. The reduction of extinction and fixation times due to inbreeding is stronger for strong selection and if alleles are either highly recessive or highly dominant. This bears implications for the effect of inbreeding on the signature of selective sweeps. These findings extend previous results obtained for random mating populations and help clarifying previous simulation and numerical results on the effect of inbreeding on the dynamics of selected alleles.     

Sequence polymorphisms in wild,weedy, and cultivated rice suggest seed‐shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed‐shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ~26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.     

Isozyme Variation in a Tropical Pioneer Tree Species (Cecropia obtusifolia,Moraceae) with High Contents of Secondary Compounds1

We define 48 allozyme loci for a tropical pioneer tree species, Cecropia obtusifolia Bertol, which has high contents of secondary compounds. Our goals were to find the effects of extraction procedures on artifacts and variation in resolution of enzyme banding patterns; to explore the relationship among the variation of the loci sampled and the enzymes' molecular structure, metabolic function and substrate; to obtain estimates of the genetic variation in this species at Los Tuxtlas rain forest (México) and to explore the variation of allelic frequencies in six successive life-history stages of the species. The resolution of the isozymes bands and the actual banding pattern varied with the type and age of tissue, the collection and storage procedures, the extraction buffer, and other loading and running procedural details. However, artifactual variation was eliminated with a new extraction buffer for species with high contents of secondary compounds. Of the 26 enzymes resolved for C. obtusifolia, we found that enzymes with a greater number of substrates and an oligomeric quaternary structure tended to be more variable than their counterparts, but the relationship was not statistically significant. The proportion of polymorphic systems varied significantly with the metabolic pathway and the function of the enzymes. Enzymes involved in starch synthesis are significantly more variable (p < 0.05) than all others, except those involved in amino acids metabolism and the proportion of polymorphic enzymes is also significantly associated with the hnction of the enzyme, the hydrolases and isomerases are significantly more variable than lyases and oxidoreductases enzymes. The percentage of polymorphic loci for C. obtusifolia was estimated at P = 27.1%. The effective number of alleles was estimated at ne = 1.3 and ne = 2.4 for all loci and only polymorphic ones respectively and the average heterozygosity (H) for all 48 loci was estimated at H = 0.05. Allele frequencies varied throughout the life-cycle of the species, with significant differences for some alleles and loci among some life-cycle stages. “Tree seeds” allele frequencies differ significantly (P < 0.05) from “rainy dispersed seeds” in 7 of 8 loci and from “soil seeds” in Six of eight loci. Allele frequencies of all three seed categories (“tree seeds”, “rainy dispersed seeds”, and “soil seeds”) differed strongly from established individuals (seedlings, juveniles and adults), while allele frequencies of established individuals are relatively similar to one another. Seedling allele frequencies at most loci were also significantly different from those found in seeds collected from trees, seed-rain, and soil. Two alleles (at GOT-2 and FE-2) were only found in soil seeds and one allele (at LAP-2) was only found in seedlings.     

Differentiation,ageing, and terminal differentiation: A semantic analysis

The largely unsolved problems in the theoretical analysis of differentiation and ageing involve a substantial component of linguistic (semantic) difficulties. Some of these are simple traps of ambiguity, resulting from metaphorical or analogical employment of established terms—for example, “terminal differentiation” (loss of division potential in vitro) as a borrowing from “differentiation” as used by developmental biologists, or “commitment” by analogy with “determination”. Some difficulties represent a failure to adopt (at least provisionally) an operational (empirical) view—for example, failure to ask what is the nature of the evidence for the view that a fertilized ovum is totipotential, or to scrutinize the evidence for the view that cells “terminally differentiated” in vitro in a conventional medium are in fact moribund under all conditions, or to examine more closely the view that the differentiated state and the cycling state are mutually exclusive.With respect to the problem of ageing, we review some of the critical experiments on ”terminal differentiation” or “clonal senescence”. We then proceed to consider some of the models that have been proposed, including a molecular model proposed by the author which appears to overcome some of the objections to other models. Some of the models exemplify the results of what are ultimately semantic vices.The problems with which these remarks began should indeed yield to the immense and novel resources of molecular biology. But the development of complete analyses demands not only good luck and delicate technique but also critical semantic clarity and severity. Given the best tools, we shall solve major theoretical problems only if we understand quite fully what problem it is that we are trying to solve—and the history of science illustrates that this is not as elementary a matter as it sounds. For the working scientist semantics (and indeed all philosophy of science) is not an indulgence or a frill, but a basic technical resource.     

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.     

Characterization of Neurospora crassa mutant stratins deficient in adenylate cyclase activity.

Mycelial extracts from Neurospora crassa strains having any one of five different mutations of the cr-1 allele (“crisp”) exhibited an adenylate cyclase specific activity 2 to 3% of that found in wild-type strains. The enzyme deficiency seemed to be specific for the cr-1 mutation but not for the “crisp” morphology and recessive in heterocaryons carrying mutated and wild-type cr-1 alleles. The reduced adenylate cyclase activity detected in extracts from cr-1 mutants was not due to an impairment in the extraction of membranes, to a preferential inactivation of the enzyme after extraction, or to the presence of inhibitors.     

Identification of new polymorphic positions in rDNA sequences of the “intermediate” Fasciola forms

Fascioliasis is a foodborne zoonotic disease generally caused by the parasitic flukes Fasciola gigantica and Fasciola hepatica in class Trematoda. An “intermediate” Fasciola forms between F. gigantica and F. hepatica has been shown to exist. However, the relationships among F. gigantica, F. hepatica, and “intermediate” Fasciola forms remain unclear. In this study, we found five new polymorphic positions in 18S and 28S rDNAs sequences of “intermediate” Fasciola forms. According to the high-throughput sequencing results, all known 16 polymorphic positions of “intermediate” Fasciola forms show a clear and consistent tendency for F. gigantica or F. hepatica, and the percentages of the most frequently occurring bases were different in specimens. In the three ITS sequence fragments, hybrid-type base combinations of the polymorphic positions were detected, and the percentages of the most frequent base combinations were different in specimens too. In addition, interestingly, the newly detected ITS-802 position was not a traditional polymorphic position in “intermediate” Fasciola forms, and the bases in ITS-802 position are not same as the allele bases of F. gigantica or F. hepatica. Our results will be helpful to investigations into the molecular taxonomy, population genetics, and ecology of F. gigantica, F. hepatica, and “intermediate” Fasciola forms.     

Simulating direct and indirect effects of climatic changes on rare perennial plant species in fragmented landscapes

Question: How does climate change influence plant species population dynamics, their time to extinction, and proportion of occupied habitats in a fragmented landscape? Location: Germany and Central European lowland. Methods: We apply a mechanistic general simulation model to test the response of plant functional types to direct and indirect effects of climate change. Three functional types were chosen to represent a set of well‐studied perennial plant species: Juncus atratus, Gentiana pneumonanthe and Primula veris. We link local population dynamics within a heterogeneous, fragmented landscape context. “Species spheres”, i.e. multi‐dimensional parameter ranges rather than single parameter realizations, based on field and literature data served as proxy for life stage transition parameters. Four climatic scenarios summarizing different cumulative weather effects on demographic rates and different local disturbance frequencies were run. The model predicts “time to extinction” (TE) and “proportion of occupied habitat” (POH) as regional indicators for species extinction risk. Results: TE decreased for all species when weather conditions worsened, and even more so when the frequency of local destructive events additionally increased. However, management towards fewer disturbance events could buffer the negative effect of climate to some extent. The magnitude of these responses varied with species type. POH declined with an increase in bad weather as well as with increasing disturbance frequency. The better the climatic conditions, the less severe were disturbances on population performance. Conclusions: The “species spheres” proved to be a valuable approach for predictive trends. As climate change usually also implies destructive events such as land‐use change, flooding or fire, our model on local and regional extinction risks can support conservation issues and management actions.     

The distribution of coalescence times and distances between microsatellite alleles with changing effective population size

We investigate the effects of past changes of the effective population size on the present allelic diversity at a microsatellite marker locus. We first derive the analytical expression of the generating function of the joint probabilities of the time to the Most Recent Common Ancestor for a pair of alleles and of their distance (the difference in allele size). We give analytical solutions in the case of constant population size and the geometrical mutation model. Otherwise, numerical inversion allows the distributions to be calculated in general cases. The effects of population expansion or decrease and the possibility to detect an ancient bottleneck are discussed. The method is extended to samples of three and four alleles, which allows investigating the covariance structure of the frequencies f(k) of pairs of alleles with a size difference of k motifs, and suggesting some approaches to the estimation of past demography.