Inferring the evolutionary history of Drosophila americana and Drosophila novamexicana using a multilocus approach and the influence of chromosomal rearrangements in single gene analyses

The evolutionary history of closely related organisms can prove sometimes difficult to infer. Hybridization and incomplete lineage sorting are the main concerns; however, genome rearrangements can also influence the outcome of analyses based on nuclear sequences. In the present study, DNA sequences from 12 nuclear genes, for which the approximate chromosomal locations are known, have been used to estimate the evolutionary history of two forms of Drosophila americana ( Drosophila   americana americana and Drosophila americana texana ) and Drosophila novamexicana ( virilis group of species). The phylogenetic analysis of the combined data set resulted in a phylogeny showing reciprocal monophyly for D. novamexicana and D. americana . Single gene analyses, however, resulted in incongruent phylogenies influenced by chromosomal rearrangements. Genetic differentiation estimates indicated a significant differentiation between the two species for all genes. Within D. americana , however, there is no evidence for differentiation between the chromosomal forms except at genes located near the X/4 fusion and Xc inversion breakpoint. Thus, the specific status of D. americana and D. novamexicana is confirmed, but there is no overall evidence for genetic differentiation between D. a. americana and D. a. texana , not supporting a subspecific status. Based on levels of allele and nucleotide diversity found in the strains used, it is proposed that D. americana has had a stable, large population during the recent past while D. novamexicana has speciated from a peripheral southwestern population having had an ancestral small effective population size. The influence of chromosomal rearrangements in single gene analyses is also examined.     

The exact values of the probability of fixation of underdominant chromosomal rearrangements.

A numerical analysis of the probability of fixation of a chromosomal mutation with partial sterility of the heterozygote in a single population is performed. Three different genetic models are considered: the first model entails constant selection against the heterozygote and is the model almost universally used in previous works; in the other two models selection against the heterozygote depends on its frequency. The exact values of the fixation probability are found by iterating transition matrices with genotype specification. Differences in results among models are small. The exact values found in the first model are compared to estimates obtained from approximations. Solutions based on diffusion models give good approximations when selection against the heterozygote is low, especially if the population is very small. For the higher values of the selection coefficient against the heterozygote, the estimates are rather imprecise, especially when the populations are not very small.     

Quantitative evaluation of chromosomal rearrangements in gene-edited human stem cells by CAST-Seq

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The fixation probability of a beneficial allele in a population dividing by binary fission

We derive formulae for the fixation probability, P, of a rare benefical allele segregating in a population of fixed size which reproduces by binary fission, in terms of the selection coefficient for the beneficial allele, s. We find that an earlier result P 4s does not depend on the assumption of binary fission, but depends on an assumption about the ordering of events in the life cycle. We find that P 2s for mutations occurring during chromosome replication and P 2.8s for mutations occurring at random times between replication events.     

The fixation probability of two competing beneficial mutations

Suppose that a beneficial mutation is undergoing a selective sweep when another beneficial mutation arises at a linked locus. We study the fixation probability of the double mutant, i.e., one (produced by recombination) that carries both mutations. Previous analysis works well for the case where the earlier beneficial mutation confers a greater selective advantage than the later mutation, but not so well in the opposite case. We present an approach to approximating the fixation probability in the case where the later mutation confers a greater selective advantage.     

The evolution of unusual chromosomal systems in sciarid flies: intragenomic conflict and the sex ratio

A model is presented for the evolution of the sciarid chromosomal system. In this model, a driving X chromosome caused female-biased sex ratios. The drive was exploited by maternal autosomes that segregated with the X at spermatogenesis. Genes in mothers converted some of their XX daughters into sons by eliminating a paternal X from the embryonic soma. L chromosomes were derived from X chromosomes and favored male-biased sex ratios. An X' chromosome arose that suppressed the effects of L chromosomes. The 1:1 sex ratio is a stalemate between the X' and X'X mothers causing all-female broods and the L chromosomes in XX mothers causing all-male broods. Any element (such as an L chromosome) that is preferentially transmitted through one sex will be selected to bias the sex ratio towards this sex.     

Chromosomal rearrangements and genetic structure at different evolutionary levels of the Sorex araneus group

Robertsonian (Rb) fusions received large theoretical support for their role in speciation, but empirical evidence is often lacking. Here, we address the role of Rb rearrangements on the genetic differentiation of the karyotypically diversified group of shrews, Sorex araneus. We compared genetic structure between 'rearranged' and 'common' chromosomes in pairwise comparisons of five karyotypic taxa of the group. Considering all possible comparisons, we found a significantly greater differentiation at rearranged chromosomes, supporting the role of chromosomal rearrangements in the general genetic diversification of this group. Intertaxa structure and distance were larger across rearranged chromosomes for most of the comparisons, although these differences were not significant. This last result could be explained by the large variance observed among microsatellite-based estimates. The differences observed among the pairs of taxa analysed support the role of both the hybrid karyotypic complexity and the level of evolutionary divergence.     

Effects of dominance on the probability of fixation of a mutant allele

We consider whether the fixation probability of an allele in a two-allele diploid system is always a monotonic function of the selective advantage of the allele. We show that while this conjecture is correct for intermediate dominance, it is not correct in general for either overdominant or underdominant alleles, and that for some parameter ranges the fixation probability can initially decrease and then increase as a function of the amount of selection. We have partial results that characterize the ranges of parameters for which this happens.      

Chromosomal rearrangements as the source of variation in the number of chromosomes in Pseudis (Amphibia, Anura)

A cytogenetic study of Pseudis specimens from three localities in Rio Grande do Sul State, the southernmost Brazilian, was performed to identify karyotypic characteristics that could account for differences in vocalization pattern and body size. Individuals from around Tainhas were compared to those of São Jerônimo and Eldorado do Sul. Specimens from these latter two localities were identified as Pseudis minuta, while those from the former were classified as Pseudis sp. (aff. minuta). The populations from São Jerônimo and Eldorado do Sul had 2n?=?24 chromosomes, classified as metacentric, submetacentric and subtelocentric. The population from Tainhas had 2n?=?28 chromosomes, with four pairs of telocentric chromosomes. Modelling of these 28 chromosomes and testing for fusion in the centromeric/telomeric regions yielded a karyotype of 2n?=?24 chromosomes, similar to that of the other populations. The similarity was reinforced by the location of the NORs and heterochromatin. The Tainhas population showed an increase in heterochromatin, as seen by the presence of additional C-bands, especially in the telocentric chromosomes. These data suggest that the two karyotypes described in this work had a common ancestry. There is evidence that the differentiation of these karyotypes may have occurred by chromosome fission and heterochromatin addition. Based on the present karyotype (2n?=?28) and on morphological and vocalization studies by other researchers, we conclude that the Tainhas population may represent a new species.     

Model and test in a fungus of the probability that beneficial mutations survive drift

Determining the probability of fixation of beneficial mutations is critically important for building predictive models of adaptive evolution. Despite considerable theoretical work, models of fixation probability have stood untested for nearly a century. However, recent advances in experimental and theoretical techniques permit the development of models with testable predictions. We developed a new model for the probability of surviving genetic drift, a major component of fixation probability, for novel beneficial mutations in the fungus Aspergillus nidulans, based on the life-history characteristics of its colony growth on a solid surface. We tested the model by measuring the probability of surviving drift in 11 adapted strains introduced into wild-type populations of different densities. We found that the probability of surviving drift increased with mutant invasion fitness, and decreased with wild-type density, as expected. The model accurately predicted the survival probability for the majority of mutants, yielding one of the first direct tests of the extinction probability of beneficial mutations.     

Chromosomal rearrangements and their role in spontaneous immortalization and transformation of rat embryo cells in vitro

Peculiarities of chromosomal rearrangements were studied in cells of the spontaneously immortalized LRec-1 and LRec-3 lines derived from rat embryo fibroblasts, as well as in LRec-1k clone cells and LRec-1sf line cells with autocrine regulation of proliferation at various cell transformation stages. The lines were obtained from rat embryo fibroblasts by cloning during rapid aging of the cultures. Using the G-banding of chromosomes, it was shown that in the process of transformation, cells of the LRec-1 and LRec-3 lines as well as of LRec-1sf maintained diploidy and specific clonal rearrangements of chromosomes 7 and 19, which were revealed earlier at the immortalization stage. In the LRec-1 cells, new clonal rearrangements of chromosomes 10 and 20 were observed, while rearrangements of chromosomes 1, 2, 11, 15, 18, and 19 were observed in the LRec-1sf cells. In the LRec-3 cells, as well as in cells of the LRec-1k clone, new chromosome rearrangements were absent. Loci involved in chromosomal rearrangements were compared with the genes located in them according to RATMAP data. The role of rearrangements of chromosomes 7 and 19 in the immortalization and malignant transformation of embryo fibroblasts is discussed, as well as the roles of other chromosomes during acquisition of the specific signs of the transformed phenotype by the LRec-1 and LRec-1sf cells.     

The effect of population structure on the rate of evolution

Ecological factors exert a range of effects on the dynamics of the evolutionary process. A particularly marked effect comes from population structure, which can affect the probability that new mutations reach fixation. Our interest is in population structures, such as those depicted by ‘star graphs’, that amplify the effects of selection by further increasing the fixation probability of advantageous mutants and decreasing the fixation probability of disadvantageous mutants. The fact that star graphs increase the fixation probability of beneficial mutations has lead to the conclusion that evolution proceeds more rapidly in star-structured populations, compared with mixed (unstructured) populations. Here, we show that the effects of population structure on the rate of evolution are more complex and subtle than previously recognized and draw attention to the importance of fixation time. By comparing population structures that amplify selection with other population structures, both analytically and numerically, we show that evolution can slow down substantially even in populations where selection is amplified.     

The probability of matching genetic markers in different samples

Hypervariable DNA polymorphisms in humans have been introduced in forensic science for the exclusion of innocent persons, and possibily for the identification of guilty ones, through mismatches and matches of DNA patterns in incriminating samples. Under the assumption of random mating and linkage equilibrium, it is observed that the probability of mismatch, then of exclusion of innocent persons, is very high. The probability of a match on the contrary may be very low, particularly when several hypervariable DNA polymorphisms are used for the DNA pattern. When a match is observed, and the probability of match is calculated, and it is lower than one in five billions, this might be considered incriminating by a judge. It is concluded that an innocent person has all advantages in submitting to the DNA fingerprinting test.     

The probability of fixation of a single mutant in an exchangeable selection model

The Cannings exchangeable model for a finite population in discrete time is extended to incorporate selection. The probability of fixation of a mutant type is studied under the assumption of weak selection. An exact formula for the derivative of this probability with respect to the intensity of selection is deduced, and developed in the case of a single mutant. This formula is expressed in terms of mean coalescence times under neutrality assuming that the coefficient of selection for the mutant type has a derivative with respect to the intensity of selection that takes a polynomial form with respect to the frequency of the mutant type. An approximation is obtained in the case where this derivative is a continuous function of the mutant frequency and the population size is large. This approximation is consistent with a diffusion approximation under moment conditions on the number of descendants of a single individual in one time step. Applications to evolutionary game theory in finite populations are presented.      

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

Chromosome rearrangements in Pectinidae (Bivalvia: Pteriomorphia) implied based on chromosomal localization of histone H3 gene in four scallops

Chromosomal structural rearrangement in four scallops, Chlamys farreri (n = 19), Patinopecten yessoensis (n = 19), Chlamys nobilis (n = 16) and Argopecten irradians (n = 16), was studied by fluorescence in situ hybridization using histone H3 gene probes. The results show that histone H3 gene sites differ strikingly with regard to number, location, and intensity among, or even within these species. For example, two histone H3 gene loci were detected on the metaphase chromosomes of P. yessoensis, while one locus was found in the others. In P. yessoensis, differing intensities of hybridization signals were detected between homologues 5 and 11, and within homologue 11. These data suggest that the histone H3 gene is a qualified chromosome marker for the preliminary understanding of the historical chromosomal reconstructing of the Pectinidae family. The variable distribution patterns of the histone H3 gene suggest that gene duplication/diminution as well as chromosome rearrangements by inversion and translocation may have played important roles in the genomic evolution of Pectinidae. We also compiled our present results with former published data regarding the chromosome mapping of rDNAs in species of the Pectinidae family. Such comparative chromosomal mapping should improve our understanding of historical chromosomal reconstructions of modern-day scallops.     

The influence of nitrate supply on nitrogen fixation during growth of the field bean Vicia faba in sand

Field bean (Vicia faba L.) cv. Maris Bead seeds were inoculated with Rhizobium Catalogue No. 1001, supplied by Rothamsted Experimental Station and grown in sand culture supplied with ¹⁵N-labelled nitrate at two concentrations. Plants were sampled at intervals throughout their growth for ¹⁵N and total N analysis. The rate of nitrate uptake was almost uniform up to pod-fill and was proportional to the nitrate concentration. Nodule weight was slightly depressed by the larger nitrate concentration at all samplings, and there was a corresponding reduction in the amount of atmospheric nitrogen fixed. However, at harvest the bean seeds from plants given most nitrate contained slightly more total N, as the enhanced nitrate uptake outweighed the reduction in fixation.     

Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates

The appearance of the vertebrates demarcates some of the most far-reaching changes of structure and function seen during the evolution of the metazoans. These drastic changes of body plan and expansion of the central nervous system among other organs coincide with increased gene numbers. The presence of several groups of paralogous chromosomal regions in the human genome is a reflection of this increase. The simplest explanation for the existence of these paralogies would be two genome doublings with subsequent silencing of many genes. It is argued that gene localization data and the delineation of paralogous chromosomal regions give more reliable information about these types of events than dendrograms of gene families as gene relationships are often obscured by uneven replacement rates as well as other factors. Furthermore, the topographical relations of some paralogy groups are discussed.     

The influence of Trypanosoma brucei infection on local immunoglobulin responses of rats to Nippostrongylus brasiliensis

Wedrychowicz H., Maclean J. M. and Holmes P. H., 1984. The influence of Trypanosoma brucei infection on local immunoglobulin responses of rats to Nippostrongylus brasiliensis. International Journalfor Parasitology14: 453–458. Serum, intestinal and lung immunoglobulin and antibody isotype responses to Nippostrongylus brasiliensis infection were studied in normal and trypanosome-infected Hooded Lister rats. Rats which received trypanosomes 7 days before N. brasiliensis infection had impaired responses of serum IgG and IgA. Bronchial and intestinal mucosal IgG was not reduced whilst IgA concentration in these sites was markedly diminished. Total immunoglobulin M levels in T. brucei parasitised rats were higher in both sera and mucosal sites. However, tests with radiolabelled adult nematode excretory-secretory antigens indicated that specific lung and intestinal IgM responses were reduced. Immunoglobulin A antibody responses were diminished most markedly in sera and lungs and also in the intestine while IgG antibodies were decreased in sera and intestine mucosae T. brucei infected rats had higher worm burdens than rats infected with N. brasiliensis alone but worm expulsion was not delayed. The results indicate that local as well as systemic antibody responses are reduced in trypanosome infected animals.     

A compact result for the time-dependent probability of fixation at a neutral locus

A result is derived, in the form of a sum, for the time-dependent probability of fixation of an unlinked neutral locus. The result captures many of the key features of the probability of fixation in a highly compact form. For ‘small’ times (t?4N_e) a single term of the sum accurately determines the time-dependent probability of fixation. This is in contrast to the well-known result of Kimura, which requires the contribution of many terms in a different sum, for ‘small’ times. Going beyond small times, an approximation is derived for the time-dependent probability of fixation which applies for all times when the initial relative allele frequency is small.