Migration-selection balance at multiple loci and selection on dominance and recombination

A steady influx of a single deleterious multilocus genotype will impose genetic load on the resident population and leave multiple descendants carrying various numbers of the foreign alleles. Provided that the foreign types are rare at equilibrium, and that all immigrant genes will eventually be eliminated by selection, the population structure can be inferred explicitly from the deterministic branching process taking place within a single immigrant lineage. Unless the migration and recombination rates were high, this simple method was a very close approximation to the simulated migration-selection balance with all possible multilocus genotypes considered.Comment: includes 6 figures and a Supporting Information. Mathematica notebook where the numerical results were obtained is available upon reques

Dinámica estacional de ocurrencia y tamaño de grupo de tres especies de cetáceos (Delphinidae y Phocoenidae) en la costa suroeste del mar Negro

The spatial and temporal occurrence of cetaceans in the Black Sea and particularly along its southwestern coastline is poorly studied. Based on a total of 609 encounters, we present the analysis of monthly dynamics of (1) the numbers of cetacean sightings and (2) their group size for all three Black Sea cetacean species: the bottlenose dolphin (Tursiops truncatus), the short-beaked common dolphin (Delphinus delphis) and the harbour porpoise (Phocoena phocoena) over a continuous period of 29 months (January 2018 - May 2020) from two fixed coastal observation points near the city of Zonguldak, Turkey. Seasonal fluctuations were found in the occurrence of all three species, with peaks in April-May (spring). Similarly, the largest groups of P. phocoena and T. truncatus were recorded in the late spring and early summer period, while D. delphis had a peak in July (summer). In case of the harbour porpoise, we speculate that these variations can be explained by the annual migrations from the northwestern to southern waters of the Black Sea, while the seasonal dynamics of the two Delphinidae species might depend on fish prey availability. While our data were collected locally, the results provide better insight into the ecology of cetaceans within the entire Black Sea.La presencia espacial y temporal de cetáceos en el mar Negro, particularmente a lo largo de su costa suroeste, está poco estudiada. Con base en un total de 609 encuentros, presentamos el análisis de la dinámica mensual de (1) el número de avistamientos de cetáceos y (2) el tamaño del respectivo grupo, para las tres especies de cetáceos del mar Negro: el delfín mular (Tursiops truncatus), el delfín común (Delphinus delphis) y la marsopa común (Phocoena phocoena), durante un período continuo de 29 meses (entre enero de 2018 y mayo de 2020) desde dos puntos de observación costeros fijos cerca de la ciudad de Zonguldak, Turquía. Se encontraron fluctuaciones estacionales en la ocurrencia de las tres especies, con picos en abril-mayo (primavera). Los grupos más grandes de P. phocoena y T. truncatus se registraron a fines de la primavera y principios del verano, mientras que los de D. delphis tuvieron un pico en julio (verano). En el caso de las marsopas comunes, especulamos que estas variaciones pueden explicarse por las migraciones anuales desde las aguas del noroeste al sur del Mar Negro, mientras que la dinámica estacional de las dos especies de Delphinidae podría depender de la disponibilidad de peces para captura. Si bien nuestros datos se recopilaron localmente, los resultados brindan una mejor comprensión de la ecología de los cetáceos en todo el mar Negro

The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes

Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role promoting gene duplication. Our findings also suggest that gene family expansions, especially in the mouse genome, undergo two phases. The first phase is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Altogether we provide evidence of the contribution of retrotransposons to the expansion and evolution of gene families. Our findings emphasize the putative importance of these elements in diversification and adaptation in the human and mouse lineages

Altitudinal Effects on Innate Immune Response of a Subterranean Rodent.

Solak HM, Yanchukov A, Colak F, et al. Altitudinal Effects on Innate Immune Response of a Subterranean Rodent. Zoological science. 2020;37(1):31-41.Immune defense is costly to maintain and deploy, and the optimal investment into immune defense depends on risk of infection. Altitude is a natural environmental factor that is predicted to affect parasite abundance, with lower parasite abundance predicted at higher altitudes due to stronger environmental stressors, which reduce parasite transmission. Using high and low altitude populations of the Turkish blind mole-rat (TBMR) Nannospalax xanthodon, we tested for effects of altitude on constitutive innate immune defense. Field studies were performed with 32 wild animals in 2017 and 2018 from two low- and one high-altitude localities in the Central Taurus Mountains, at respective altitudes of 1010 m, 1115 m, and 2900 m above sea level. We first compared innate standing immune defense as measured by the bacteria-killing ability of blood serum. We then measured corticosterone stress hormone levels, as stressful conditions may affect immune response. Finally, we compared prevalence and intensity of gastrointestinal parasites of field-captured TBMR. We found that the bacteria-killing ability of serum is greater in the mole-rat samples from high altitude. There was no significant difference in stress (corticosterone) levels between altitude categories. Coccidian prevalence and abundance were significantly higher in 2017 than 2018 samples, but there was no significant difference in prevalence, abundance, or intensity between altitudes, or between sexes. Small sample sizes may have reduced power to detect true differences; nevertheless, this study provides support that greater standing innate immunity in high altitude animals may reflect greater investment into constitutive defense

One- and Two-Locus Population Models With Differential Viability Between Sexes: Parallels Between Haploid Parental Selection and Genomic Imprinting

A model of genomic imprinting with complete inactivation of the imprinted allele is shown to be formally equivalent to the haploid model of parental selection. When single-locus dynamics are considered, an internal equilibrium is possible only if selection acts in the opposite directions in males and females. I study a two-locus version of the latter model, in which maternal and paternal effects are attributed to the single alleles at two different loci. A necessary condition for the allele frequency equilibria to remain on the linkage equilibrium surface is the multiplicative interaction between maternal and paternal fitness parameters. In this case the equilibrium dynamics are independent at both loci and results from the single-locus model apply. When fitness parameters are additive, analytic treatment was not possible but numerical simulations revealed that stable polymorphism characterized by association between loci is possible only in several special cases in which maternal and paternal fitness contributions are precisely balanced. As in the single-locus case, antagonistic selection in males and females is a necessary condition for the maintenance of polymorphism. I also show that the above two-locus results of the parental selection model are very sensitive to the inclusion of weak directional selection on the individual's own genotypes

Genotype fitness as a function of the block length.

<p>The fitness of the genotype is plotted against the proportion of the chromosome occupied by the foreign genes: corresponds to additive fitness (no epistasis), while and represent the positive and the negative epistasis, correspondingly. The points indicate the fitness of the initial block carrying 4 genes at . Point 1: <i>n</i> = 10, fitness is calculated according to eq. 12. Point 2: <i>n</i> = 10, fitness is rescaled by the length of the initial block. Point 3: initial block carries the maximum number of genes, .</p

A subset of the lineage descending from an immigrant haplotype

<p><b> carrying 10 genes.</b> After selection, the genotypes carrying foreign genes (solid black dots) recombine with the resident genotypes (shown as the rows of open dots), so that the average number of foreign alleles per genotype is reduced every generation . Once recombination has broken the foreign genotype down to one gene, it is certain to eventually be eliminated by selection in the single foreign allele state.</p

Schematic representation of the terms in Eqs (1) and (2).

<p><b>A</b> – representing the mean population fitness from the branching process within foreign lineages. The future load caused by the independent lineages (white contour) is subtracted from the fitness contribution of the migrants, measured at the generation of sampling (contour filled by dark grey). Note that the proportion of migrants culled before reproduction, , is not a part of the mean population fitness. <b>B</b> – Dynamics of the lineage size, , determined by the Eq. (2). is reduced by migration and selection, but increased as the foreign genotype recombines and gives rise to sub-lineages. Note that the term , i.e. the contribution of the individuals culled by selection, is included in the lineage size calculation.</p