Group selection on the boundary of a stable population

This article presents a model of group selection via differential extinction acting on small boundary populations of a large, fixed population. We restrict consideration to extinction of populations at or near habitat carrying capacity, thus modeling the kind of situation envisioned by Wynne-Edwards (1962). Under the assumption that the extinction rate is large relative to individual genetic parameters, we discuss the effect of differential extinction on the distribution of gene frequencies within boundary micropopulations. In these circumstances, it is shown that differential extinction is most likely to produce a bimodal distribution of the gene frequencies if the form of the extinction operator approximates a step function, with a critical allele frequency at which the extinction rate shifts from high to low. The need for a rather close approximation to such discontinuous behavior limits the possible conditions under which differential extinction might be important. We conclude with a comparison of our model with that of Levins (1970a) and suggest some technically feasible generalizations of our approach.     

Gene extinction and allelic origins in complex genealogies

With the increasing emphasis on data analysis in mathematical genetics, problems of parametrizing genealogical structure become of practical importance. A complete specification of the genetic effects of genealogical structure is provided by the probabilities of genetically distinct states of gene identity by descent. Although this provides a direct parametrization for the joint distribution of traits on a set of related individuals, it is an unwieldy tool in the analysis of large and complex genealogies. Probabilities of joint descent of founder genes and likely ancestries of alleles provide alternative characterizations of relationship and have direct application in practical problems. Joint extinction probabilities of founder genes can also be derived as ancestral likelihoods: evolutionarily, the most significant characteristic of a genealogical structure must be its effect on the survival and extinction of genes.     

Population genetics and distribution data reveal conservation concerns to the sky island endemic <Emphasis Type="Italic">Pithecopus megacephalus</Emphasis> (Anura,Phyllomedusidae)

Pithecopus megacephalus is a reticulated monkey–frog species endemic to the highlands of the Espinhaço Mountain Range in southeastern Brazil, an important centre of endemism in South America. This species has a discontinuous distribution and is considered “data-deficient” by the IUCN Red List, raising concerns about its conservation. Understanding the historical dynamics and connectivity of P. megacephalus populations can provide guidelines for preservation of this species in the wild. To investigate the population dynamics of P. megacephalus, we obtained multilocus DNA data for 55 individuals from different locations along the species’ known distribution. Spatial population structure, genetic diversity and demographic parameters were evaluated using population genetic and phylogeographical tools. We also evaluated its extent of occurrence and area of occupancy to investigate extinction risk of this species. We found genetic structure along P. megacephalus’ spatial distribution in the South Espinhaço Mountain Range corresponding to three population groups: northern, central and southern. Our results could provide important data on geographic distribution and population dynamics for a Data Deficient species. Therefore, we suggest these population data, together with the species’ limited occurrence in sky island environments could be used for a more accurate classification of P. megacephalus in the IUCN list, and conservation strategies for the species should be planned accordingly.     

The survival of micromycetes exposed to space conditions

Original data on the survival of fungal spores exposed to space conditions are presented. The experiment was carried out on the Earth-orbiting Russian satellite Foton-M4. The flight duration of the satellite was 45 days. Thirteen fungal species (hyaline as well as pigmented) from 10 genera recovered from destructed stone materials were studied. Sterile quartz sand was inoculated by the fungal spores and was placed into Eppendorf tubes. During the space flight, the Eppendorf tubes with fungal spores were kept inside the Foton descent capsule in the “Biokont” containers and on the external surface of the capsule in the “Exobiofrost” containers exposed to the open space as well. Spores of ten species (77% of all tested species), i.e. Acremonium charticola, Aspergillus niger, Aspergillus versicolor, Chaetomium globosum, Cladosporium sphaerospermum, Penicillium chrysogenum, Penicillium verrucosum, Purpureocillium lilacinum, Sarocladium kiliense, and Trichoderma harzianum, survived after the flight both inside and outside the descent capsule. Only three species (23% of all tested species), i.e. Acremonium furcatum, Engyodontium album and Verticillium zaregamsianum, failed to survive outside as well as inside the capsule. Spore viability differed depending on the fungal species. Thus, spores of some fungal species are able to survive under the complex of stress factors such as low temperature values, radiation, etc. We have shown that micromycetes can be used as a model group for study of eukaryotic organisms’ resistance to stress factors, due to their high tolerance not only to extreme terrestrial environments, but to the extraterrestrial ones as well.     

Efficient QTL detection of flowering date in a soybean RIL population using the novel restricted two-stage multi-locus GWAS procedure

Key message

Eighty-six R1 QTLs accounting for 89.92% phenotypic variance in a soybean RIL population were identified using RTM-GWAS with SNPLDB marker which performed superior over CIM and MLM-GWAS with BIN/SNPLDB marker.

Abstract

A population (NJRIKY) composed of 427 recombinant inbred lines (RILs) derived from Kefeng-1?×?NN1138-2 (MGII?×?MGV, MG maturity group) was applied for detecting flowering date (R1) quantitative trait locus (QTL) system in soybean. From a low-depth re-sequencing (~?0.75?×), 576,874 SNPs were detected and organized into 4737 BINs (recombination breakpoint determinations) and 3683 SNP linkage disequilibrium blocks (SNPLDBs), respectively. Using the association mapping procedures “Restricted Two-stage Multi-locus Genome-wide Association Study” (RTM-GWAS), “Mixed Linear Model Genome-wide Association Study” (MLM-GWAS) and the linkage mapping procedure “Composite Interval Mapping” (CIM), 67, 36 and 10 BIN-QTLs and 86, 14 and 23 SNPLDB-QTLs were detected with their phenotypic variance explained (PVE) 88.70–89.92% (within heritability 98.2%), 146.41–353.62% (overflowing) and 88.29–172.34% (overflowing), respectively. The RTM-GWAS with SNPLDBs which showed to be more efficient and reasonable than the others was used to identify the R1 QTL system in NJRIKY. The detected 86 SNPLDB-QTLs with their PVE from 0.02 to 30.66% in a total of 89.92% covered 51 out of 104 R1 QTLs in 18 crosses in SoyBase and 26 out of 139 QTLs in a nested association mapping population, while the rest 29 QTLs were novel ones. From the QTL system, 52 candidate genes were annotated, including the verified gene E1, E2, E9 and J, and grouped into 3 categories of biological processes, among which 24 genes were enriched into three protein–protein interaction networks, suggesting gene networks working together. Since NJRIKY involves only MGII and MGV, the QTL/gene system among MG000–MGX should be explored further.

     

Landscape genetics in the subterranean rodent <Emphasis Type="Italic">Ctenomys</Emphasis> “<Emphasis Type="Italic">chasiquensis</Emphasis>” associated with highly disturbed habitats from the southeastern Pampas region,Argentina

Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys “chasiquensis”, a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. “chasiquensis” are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.     

microRNA-mediated <Emphasis Type="Italic">R</Emphasis> gene regulation: molecular scabbards for double-edged swords

Plant resistance (R) proteins are immune receptors that recognize pathogen effectors and trigger rapid defense responses, namely effector-triggered immunity. R protein-mediated pathogen resistance is usually race specific. During plant-pathogen coevolution, plant genomes accumulated large numbers of R genes. Even though plant R genes provide important natural resources for breeding disease-resistant crops, their presence in the plant genome comes at a cost. Misregulation of R genes leads to developmental defects, such as stunted growth and reduced fertility. In the past decade, many microRNAs (miRNAs) have been identified to target various R genes in plant genomes. miRNAs reduce R gene levels under normal conditions and allow induction of R gene expression under various stresses. For these reasons, we consider R genes to be double-edged “swords” and miRNAs as molecular “scabbards”. In the present review, we summarize the contributions and potential problems of these “swords” and discuss the features and production of the “scabbards”, as well as the mechanisms used to pull the “sword” from the “scabbard” when needed.     

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?     

Methods to estimate effective population size using pedigree data: Examples in dog,sheep, cattle and horse

Background

Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.

Results

Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusions

When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.     

Strategies of seed dispersal and germination in plants inhabiting deserts

Massive seed consumption is typical in many deserts. The “escape” or “protection” strategies of seed dispersal are important, as they prevent massive seed consumption. The more extreme the desert, the more unpredictable the low amounts and distribution of the rains as well as the beginning and length of the season or seasons with rains. Seeds, which have the highest resistance to extreme environmental conditions, develop during germination into seedlings, which are the most sensitive. Therefore, germination of parts of the seed population at their respective proper times spreads the risk over time and is thus very important for plant survival, especially in those plants inhabiting the more extreme deserts. Each of the plant species studied was found to have its own survival strategies of seed dispersal and germination. At least two extreme seed-dispersal and germination strategies have been observed: 1) the “escape” seed dispersal and “opportunistic” portioned seed-germination strategies, such as inSchismus arabicas andSpergularia diandra, and 2) the “cautious” portioned dispersal by rain of the protected seeds, such as inAsteriscus hierochunticus and portioned dispersal and rapid germination strategies such as inBlepharis spp. The fate of future generations, as far as the germinability of seeds of some species is concerned, depends on the influences of maternal and environmental factors when the seeds are still on the mother plant, mostly during the final stage of seed maturation, as inTrigonella arabica. It may even depend on the position of the caryopsis from which the mother plant originated, as inAegilops geniculata. The dry post-maturation conditions and the environmental factors during seed wetting and germination may also affect the percentage of seed germination, as inSchismus arabicus.     

Models of the evolution of altruism

There are two ways of calculating the spread of a gene for altruism. One, originally proposed by Hamilton, is to allow for the effects of the gene on the survival and reproduction of collateral relatives of the individual carrying it (i.e., “inclusive fitness”); this leads to the condition k > 1/r for the spread of the gene, where k is a benefit/cost ratio. The other is to count only the direct offspring of a carrier, but to allow for the altruistic acts performed toward the carrier by its relatives (“neighbour modulated fitness” or “personal fitness”). A recent personal fitness model (L. L. Cavalli Sforza and M. W. Feldman, 1978, Theor. Pop. Biol.14, 268–280) analyses parent-offspring and sib-sib altruism and concludes that k > 1/r is applicable only when fitness components are combined additively. The present paper analyses some simple models in which the phenotypic effects are carefully specified. It is concluded that it is sometimes, but not always, appropriate to combine fitness components additively. The relative roles of inclusive and personal fitness models are compared. The former have the virtue of being easier to think about in causal terms; and the latter of incorporating the evolution of altruism into the corpus of population genetics as an example of frequency-dependent selection.     

High-throughput sequencing of <Emphasis Type="Italic">Prunus ferganensis</Emphasis> indicates that it is a geographical population of <Emphasis Type="Italic">P. persica</Emphasis>

Peach belongs to the genus Prunus, which includes Prunus persica and its relative species, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Of these, P. ferganensis have been classified as a species, subspecies, or geographical population of P. persica. To explore the genetic difference between P. ferganensis and P. persica, high-throughput sequencing was used in different peach accessions belonging to different species. First, low-depth sequencing data of peach accessions belonging to four categories revealed that similarity between P. ferganensis and P. persica was similar to that between P. persica accessions from different geographical populations. Then, to further detect the genomic variation in P. ferganensis, the P. ferganensis accession “Xinjiang Pan Tao 1” and the P. persica accession “Xia Miao 1” were sequenced with high depth, and sequence reads were assembled. The results showed that the collinearity of “Xinjiang Pan Tao 1” with the reference genome “Lovell” was higher than that of “Xia Miao 1” and “Lovell” peach. Additionally, the number of genetic variants, including single nucleotide polymorphisms (SNPs), structural variations (SVs), and the specific genes annotated from unmapped sequence in “Xia Miao 1” was higher than that in “Xinjiang Pan Tao 1” peach. The data showed that there was a close distance between “Xinjiang Pan Tao 1” (P. ferganensis) and reference genome which belong to P. persica, comparing “Xia Miao 1” (P. persica) and reference ones. The results accompany with phylogenetic tree and structure analysis confirmed that P. ferganensis should be considered as a geographic population of P. persica rather than a subspecies or a distinct species. Furthermore, gene ontology analysis was performed using the gene comprising large-effect variation to understand the phenotypic difference between two accessions. The result revealed that the pathways of gene function affected by SVs but SNPs and insertion-deletions markedly differed between the two peach accessions.     

A naturally occurring insertion in the <Emphasis Type="Italic">RsFLC2</Emphasis> gene associated with late-bolting trait in radish (<Emphasis Type="Italic">Raphanus sativus</Emphasis> L.)

Premature flowering reduces the yield and quality of the harvested fleshy taproot in radish. However, there has been little molecular marker research on the radish late-bolting trait. In this study, F₂ and F_2:3 populations derived from a cross of “Ninengo” (late-bolting) and “Maer” (early-bolting) were analyzed to map late-bolting genes. Five hundred insertion and deletion (InDel) markers were designed according to the whole-genome resequencing data of the two parents. A genetic map was constructed based on the F₂ population, and a late-bolting gene was detected in a 1.1-cM region between the markers InDel520 and InDel535 on chromosome R02 that explained the highest (76.4%) phenotypic variance. RsFLC2 was identified as a candidate gene in this region. Notably, “Ninengo” contains a 1627-bp insertion near the 5′ end of the first intron of RsFLC2. Allelic variation analyses in the F₂ population further validated that RsFLC2was associated with the late-bolting trait in radish. The expression pattern of RsFLC2 was significantly different between “Ninengo” and “Maer” during vernalization. Vernalization suppressed RsFLC2 expression, and the 1627-bp insertion in the first intron weakened gene repression in “Ninengo” plants, resulting in late-bolting. This study lays a foundation for uncovering the molecular mechanism of late-bolting and marker-assisted selection for breeding late-bolting varieties of radish.     

Gene tree parsimony for incomplete gene trees: addressing true biological loss

Motivation

Species tree estimation from gene trees can be complicated by gene duplication and loss, and “gene tree parsimony” (GTP) is one approach for estimating species trees from multiple gene trees. In its standard formulation, the objective is to find a species tree that minimizes the total number of gene duplications and losses with respect to the input set of gene trees. Although much is known about GTP, little is known about how to treat inputs containing some incomplete gene trees (i.e., gene trees lacking one or more of the species).

Results

We present new theory for GTP considering whether the incompleteness is due to gene birth and death (i.e., true biological loss) or taxon sampling, and present dynamic programming algorithms that can be used for an exact but exponential time solution for small numbers of taxa, or as a heuristic for larger numbers of taxa. We also prove that the “standard” calculations for duplications and losses exactly solve GTP when incompleteness results from taxon sampling, although they can be incorrect when incompleteness results from true biological loss. The software for the DP algorithm is freely available as open source code at https://github.com/smirarab/DynaDup.

     

Electrical-ionic control of gene expression

• 1.1. Changes in turgor, in cell volume, in membrane potential, in intracellular ionic activities and, more recently, in spontaneous electrical activity have been reported to be causally linked to the expression of specific genes.
• 2.2. As a result, it has become clear that changes in membrane properties and/or in the intracellular “ionic environment” can play an important role in generating cell type specific physiological responses which indirectly—or maybe directly—affect gene expression.
• 3.3. Possible targets of the ionic “environment” are: the selective transport across biological membranes; the activity of certain (regulatory) enzymes; the conformation of some (regulatory) proteins; of chromatin; of the cytoskeleton; of the nuclear matrix; the association of the cytoskeleton with plasmamembrane proteins or RNA; the association chromatin-nuclear matrix; protein-DNA and protein-protein interactions etc. All these sites may be instrumental to “fine or coarse” tuning of gene expression.
• 4.4. The exact mechanisms by which changes in intracellular ionic environment are transduced, directly or indirectly, into alterations of the activity of trans-acting factors have not yet been fully uncovered. Changes in the degree of phosphorylation of regulatory proteins and/or of trans -acting factors may provoke fine tuning effects on cell type specific gene expression activity.
• 5.5. The intranuclear ionic environment is difficult to measure in an exact way. It can be influenced in a number of ways. The location of a gene, as determined by the position of the nucleus in the cytoplasm and by the association of chromatin to the nuclear matrix may be especially important in cells which can generate some type of intracellular gradient or in excitable cells.
• 6.6. In some somatic cell types—germinal vesicles may behave differently—the intranuclear inorganic ionic “environment” has been reported to be distinct from the cytoplasmic one. This challenges the widespread assumption that the nuclear envelope is always freely permeable to small molecules and inorganic ions.
• 7.7. It can be expected that the fast progress in the cloning of “electrically” controlled genes, in the identification of trans-acting factors, in their mode of interaction with genes and in the precise localization of genes within the nucleus may soon lead to substantial progress in this domain.

     

Fine mapping <Emphasis Type="Italic">Ruv2</Emphasis>, a new rust resistance gene in cowpea (<Emphasis Type="Italic">Vigna unguiculata</Emphasis>), to a 193-kb region enriched with NBS-type genes

Key message

A new rust resistance gene Ruv2 was fine-mapped in cowpea to a 193-kb region on chromosome 2, which harboured 23 predicted gene models enriched with NBS-type genes.

Abstract

ZN016 is a landrace vegetable cowpea highly resistant to rust. Two previous studies using mixed-spores inoculation suggested different modes of inheritance of rust resistance in ZN016. In this study, we initially developed a detached leaf assay with a purified single-rust isolate (Auv-LS). Using this approach, we assessed the inheritance of rust resistance in a recombinant inbred line (RIL) population and an F₂ population, both derived from the cross of “ZN016” and the susceptible cultivar “Zhijiang282.” A single dominant gene mode against Auv-LS was revealed in both populations. QTL mapping showed that this gene was coincident with the Ruv2 locus on LG7, one of the three resistance QTLs previously mapped based on mixed-spores inoculation data. Therefore, Ruv2 was considered as specifically against the rust isolate Auv-LS. Through an analysis of the RIL recombinants at Ruv2, we fine-mapped the gene to an ~?0.45-cM interval between SNP markers 2_09656 and 2_00973, which corresponded to an ~?193-kb region on chromosome 2 that harboured 23 predicted gene models enriched with NBS-type genes. Re-sequencing of the two parents revealed polymorphisms in four genes predictively to cause substantial protein structural changes, rendering them valuable candidate genes for future validation. Cross-species syntenic analysis indicated that Ruv2 may represent a novel rust resistance gene in food legumes. A cleaved amplified polymorphic sequences marker tightly linked to Ruv2 was developed to facilitate breeding. This work establishes a basis for map-based cloning of Ruv2 and breeding for rust resistance in cowpea and other legume crops.

     

Direct sequencing of PCR-amplified DNA

This article describes the direct sequencing of PCR-amplified DNA, a technique that bypasses the problem of replication errors sometimes associated with other PCR procedures. The direct sequencing procedure produces an “average sequence” of all the copies of the target. Any miscopied molecule usually represents only a small proportion of the total. The technique described here is based on the “traditional” ddNTP sequencing method of Sanger et al.     

Possible contribution of quantum-like correlations to the placebo effect: consequences on blind trials

Background

Factors that participate in the biological changes associated with a placebo are not completely understood. Natural evolution, mean regression, concomitant procedures and other non specific effects are well-known factors that contribute to the “placebo effect”. In this article, we suggest that quantum-like correlations predicted by a probabilistic modeling could also play a role.

Results

An elementary experiment in biology or medicine comparing the biological changes associated with two placebos is modeled. The originality of this modeling is that experimenters, biological system and their interactions are described together from the standpoint of a participant who is uninvolved in the measurement process. Moreover, the small random probability fluctuations of a “real” experiment are also taken into account. If both placebos are inert (with only different labels), common sense suggests that the biological changes associated with the two placebos should be comparable. However, the consequence of this modeling is the possibility for two placebos to be associated with different outcomes due to the emergence of quantum-like correlations.

Conclusion

The association of two placebos with different outcomes is counterintuitive and this modeling could give a framework for some unexplained observations where mere placebos are compared (in some alternative medicines for example). This hypothesis can be tested in blind trials by comparing local vs. remote assessment of correlations.

     

Random disturbance and diversity of competitive systems

Population size distribution within a community of species with a competitive hierarchy, is studied. With the introduction of a stochastic model of invasion and extinction due to random environmental disturbance, the stationary population size distribution is derived as a function of the parameter, which denotes the ratio of rates of random extinction and invasion. From this result it is shown that the Shannon-type diversity takes the maximum value under the situation that 10 20 percent of habitat sites remain unoccupied, and the number of species also becomes maximum at intermediate levels of disturbance. The dynamical properties of a one-sided competitive system are also discussed by use of the Lotka-Volterra equations.     

Mathematical models for cellular systems. The von foerster equation. Part II

This is the continuation of Part I, which was published in the September, 1965, issue of theBulletin. The birth rate, α(t), is now assumed to be a linear functional of the age density,n. This gives a simple model of self-replenishing stem cell compartments, and leads to a necessary condition for the existence of a steady state. Some examples are presented to illustrate the formalism. They include: (a) An equivivant population with life spanD and no losses from death or migration. The total number of cells is multiplied by 2 in each time intervalD. As a special case, frequently realized in practice, the population may be increasing exponentially with time (“log-phase” of growth). (b) A compartment with “random” emigration of cells and gamma distribution of life spans. (c) An oversimplified version of L. G. Lajtha’s model describing stem cell kinetics. In section IV a simple case in which the loss function depends explicitly onn is discussed very briefly.