Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals

Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity–fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome‐wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.     

Allozymes and the genetics of antler development in red deer (Cervus elsphus)

In order to examine a previously hypothesized influence of selective hunting on allele frequency changes at some regularly polymorphic allozyme loci in red deer ( Cervus eluphus ), antler characters, serving as criteria for culling, were examined in relation to electrophoretic variation in two free-ranging populations of the Vosges, Eastern France, and an enclosure in Central France. When homozygous for the allele Idh-2 ¹²⁵, stags ≥ 2 years old had a significantly higher number of antler points (NAP). When homozygous for the allele Acp-2 ¹⁰⁰, stags older than 5 years had antlers that were significantly larger for a number of traits (NAP, main beam length and circumference, coronet circumference, brow tine length). Among younger stags, all antler traits in Acp-2 ¹⁰⁰ homozygotes were significantly smaller than in carriers of the alternative allele, Acp-2 ⁸⁵. Our data suggest the presence of at least two independent genetic components (one associated with early development of a high NAP, the other with generally large antler size in adults), affecting antler expression in red deer. Those genetic components, possibly major genes which are chromosomally linked with the allozyme loci studied, compensate or reinforce each other in their phenotypic effects. By playing a role in balancing benefits and costs of male reproductive success, they may be part of a genetic mechanism enabling the rapid adaptation of a population to various environmental and demographic conditions. The three populations studied originate from one another, and, based on an assessment of effective population sizes, it could be demonstrated that selective hunting for antler shape has changed allelic frequencies at the associated marker loci within a few generations.     

Growth rate correlates to individual heterozygosity in the European eel, Anguilla anguilla L

Heterozygosity-fitness correlations (HFCs) have been reported in populations of many species. We provide evidence for a positive correlation between genetic variability and growth rate at 12 allozyme loci in a catadromous marine fish species, the European eel (Anguilla anguilla L.). More heterozygous individuals show a significantly higher length and weight increase and an above average condition index in comparison with more homozygous individuals. To a lesser extent, six microsatellite loci show a similar pattern, with positive but not significant correlations between heterozygosity and growth rate. The HFCs observed could be explained by an effect of either direct allozyme over-dominance or associative overdominance. Selection affecting some of the allozyme loci would explain the greater strength of the HFCs found at allozymes in comparison with microsatellites and the lack of correlation between MLH at allozymes and MLH at microsatellites. Associative overdominance (where allozyme loci are merely acting as neutral markers of closely linked fitness loci) might provide an explanation for the HFCs if we consider that allozyme loci have a higher chance than microsatellites to be in linkage disequilibrium with fitness loci.     

Parentage testing in alpacas (Vicugna pacos) using semi-automated fluorescent multiplex PCRs with 10 microsatellite markers

The aim of this study was to assess and apply a microsatellite multiplex system for parentage determination in alpacas. An approach for parentage testing based on 10 microsatellites was evaluated in a population of 329 unrelated alpacas from different geographical zones in Perú. All microsatellite markers, which amplified in two multiplex reactions, were highly polymorphic with a mean of 14.5 alleles per locus (six to 28 alleles per locus) and an average expected heterozygosity ( H _E) of 0.8185 (range of 0.698–0.946). The total parentage exclusion probability was 0.999456 for excluding a candidate parent from parentage of an arbitrary offspring, given only the genotype of the offspring, and 0.999991 for excluding a candidate parent from parentage of an arbitrary offspring, given the genotype of the offspring and the other parent. In a case test of parentage assignment, the microsatellite panel assigned 38 (from 45 cases) offspring parentage to 10 sires with LOD scores ranging from 2.19 × 10⁺¹³ to 1.34 × 10⁺¹⁵ and Δ values ranging from 2.80 × 10⁺¹² to 1.34 × 10⁺¹⁵ with an estimated pedigree error rate of 15.5%. The performance of this multiplex panel of markers suggests that it will be useful in parentage testing of alpacas.     

Survival of κ-carrageenan-encapsulated and unencapsulated Pseudomonas aeruginosa UG2Lr cells in forest soil monitored by polymerase chain reaction and spread plating

Abstract A method was developed for direct extraction, purification and amplification of DNA from forest soil. Eighty-two % of the DNA in Pseudomonas aeruginosa UG2Lr introduced into soil was recovered. The detection limit for the strain was approximately 800 cfu g⁻¹ of dry soil based on the polymerase chain reaction (PCR). Survival of κ-carrageenan-encapsulated and unencapsulated UG2Lr was monitored by antibiotic selective and bioluminescence-based nonselective plating and PCR-amplification of a tnsA fragment. After freeze-thaw treatment of soil samples, the unencapsulated UG2Lr declined from an initial population density of 1 × 10⁹ cfu g⁻¹ of dry soil to below the detection threshold of both selective (14 cfu g⁻¹ of dry soil) and nonselective (1 × 10³ cfu g⁻¹ of dry soil) plating. However, presence of nonculturable UG2Lr cells in the soil was revealed by PCR and resuscitation of the bacteria. Population density of the encapsulated UG2Lr increased from 2.7 × 10⁶ to 2.9 × 10⁸ cfu g⁻¹ of dry soil after a 3-week incubation at 22°C and declined to 6.3 × 10⁶ cfu g⁻¹ of dry soil after the freeze-thaw treatment.     

The relative densities of red (Cervus elaphus) and roe (Capreolus capreolus) deer and their relationship in Scottish plantation forests

Population densities of red and roe deer were estimated in 20 conifer plantations throughout central and northern Scotland. Ten forests were selected on the basis of culling records that were considered likely to cover the range of possible densities. Ten further forests were selected at random to investigate the relationship between red and roe deer densities. Density assessment was by standing-crop dung-group counts, on 1.5 x 100 m transects. Dung decay rates were estimated in four areas and used to convert the values to deer densities. Red deer densities were estimated to range from 0.3-35 km⁻²; roe deer densities ranged from 0.5-25 km⁻². Preferences for different structural habitats within individual forests (i.e. blocks with different age classes of tree) were inferred from dung densities. Red deer preferred unplanted ground, open-thicket, and prethicket; roe deer likewise preferred prethicket (highly) and open-thicket. Both species avoided closed-canopy habitats. Red and roe deer densities were negatively correlated and the relationship was significant when the data were log transformed ( P < 0.05).     

Genetic effect of transportation infrastructure on roe deer populations (Capreolus capreolus)

Anthropogenic transportation infrastructure is a major factor of habitat fragmentation leading to genetic population fragmentation in wildlife. Assessing and understanding the impact of this deterministic factor on genetic diversity and divergence of populations is crucial to appraise the viability of wildlife populations in fragmented landscapes. In this study, the roe deer is used as an example species for the assessment of genetic differentiation of populations separated by an anthropogenic barrier. In order to detect genetic discontinuities, we screened 12 polymorphic microsatellites on 222 individuals out of 11 roe deer populations that were sampled on the east and the westside of a fenced motorway in Central Switzerland. The interaction between landscape structure and microevolutionary processes such as gene flow and drift were assessed and evaluated by different population genetic methods like F-statistics, Mantel test, spatial autocorrelation analyses, Monmonier algorithm, and principal component analysis in conjunction with geographic information system data (synthesis map). We revealed an influence of the transportation infrastructure on genetic divergence of the roe deer population examined, but no impact on genetic diversity was detected. Based on the achieved genetic findings, recommendations for management implementation were made.     

Heterozygosity–fitness correlations in blue tit nestlings (<Emphasis Type="Italic">Cyanistis caeruleus</Emphasis>) under contrasting rearing conditions

Understanding the relation between genetic variation and fitness remains a key question in evolutionary biology. Although heterozygosity has been reported to correlate with many fitness-related traits, the strength of the heterozygosity–fitness correlations (HFCs) is usually weak and it is still difficult to assess the generality of these associations in natural populations. It has been suggested that HFCs may become meaningful only under particular environmental conditions. Moreover, existing evidence suggests that HFCs may also differ between sexes. The aim of this study was to investigate correlations between heterozygosity in neutral markers (microsatellites) and fitness-related traits in a natural population of blue tits (Cyanistes caeruleus). Additionally, we tested whether sex and environmental conditions may influence the magnitude and direction of HFCs. We found a positive relationship between heterozygosity and body mass of 14 days post-hatching nestlings, but only among females. Our results suggest that the correlation between heterozygosity and nestling body mass observed among female offspring could be attributed to within-brood effects. We failed to find any evidence that environmental conditions as simulated by brood size manipulation affect HFCs.     

Activity patterns in moose and roe deer in a north boreal forest

The activity patterns of a coarse browser, the moose. Alces alces , and a selective browser, the roe deer, Capreolus capreolus . in a north boreal forest, central Sweden, were compared with respect to time allocated for foraging and processing (ruminating) in different seasons. Data were quantified by measuring 24 h activity patterns which included both the duration and frequency of active and inactive periods. Activity patterns were measured from 9 female moose and 9 roe deer that were radiomarked during April 1974–May 1978 (roe deer) and February 1982–December 1984 (moose). In total, data were available from 4345 h for roe deer and 14745 h for moose. Roe deer differed from moose in having active bouts more evenly distributed over the day. Generally, both species were most active during sunrise and sunset. Total daily active time varied with season, reaching the highest value in late May – early June among roe deer (56.7% of the day) and a month later among moose (51.9%). Both species were least active in February (30–40%). Average length of active bouts did not differ significantly between the species but changed with season (roe deer 48.6–99.2 min, moose 61.6–88.7 min). Average length of inactive bouts varied significantly with season, with moose having consistently longer bouts (89.3–156.3 min) than roe deer (55.8–107.0 min). The number of activity bouts per day were also higher among roe deer. During midsummer, they changed activity nearly twice as many times as moose (26 times d⁻¹ vs 16 times d⁻¹).     

Genetic and environmental influences on self-reported and parent-reported behavior problems in young adult adoptees

The aim of the present study was to estimate the genetic, shared and nonshared environmental contributions to self-reported and parent-reported internalizing and externalizing problems in a follow-up study of intercountry adopted young adults. Young Adult Self-Report ratings were obtained from 1475 adoptees aged 22–32 years and Young Adult Behavior Checklist ratings from 1115 adoptive parents. For the genetic analyses, a subset of 143 adopted biologically related and 295 unrelated siblings was used. The data were subjected to model fitting decomposing three sources of variance: genetic factors (A) shared environment (C) and nonshared environment (E). Genetic factors were of more importance in both self-reported ( A ²= 54%, C ²= 0, and E ²= 46%) and parent-reported ( A ²= 76%, C ²= 15% and E ²= 9%) internalizing problems. Environmental factors were of more importance in both self-reported ( A ²= 33%, C ²= 17% and E ²= 50%) and parent-reported ( A ²= 28%, C ²= 27% and E ²= 45%) externalizing problems. This was in contrast with findings from the first and second assessments in the same sample during adolescence when genetic factors were more important in explaining externalizing problems compared with internalizing problems. Our results suggest a developmental reversal in genetic and environmental influences on behavior problems from early adolescence into adulthood, which could be related to different underlying developmental trajectories.     

Stress-related hormones and genetic diversity in sea otters (Enhydra lutris)

Sea otters ( Enhydra lutris ) once ranged throughout the coastal regions of the north Pacific, but were extirpated throughout their range during the fur trade of the 18th and 19th centuries, leaving only small, widely scattered, remnant populations. All extant sea otter populations are believed to have experienced a population bottleneck and thus have lost genetic variation. Populations that undergo severe population reduction and associated inbreeding may suffer from a general reduction in fitness termed inbreeding depression. Inbreeding depression may result in decreased testosterone levels in males, and reduced ability to respond to stressful stimuli associated with an increase in the stress-related adrenal glucocorticoid hormones, cortisol and corticosterone. We investigated correlations of testosterone, cortisol, and corticosterone with genetic diversity in sea otters from five populations. We found a significant negative correlation between genetic diversity and both mean population-level ( r ²= 0.27, P < 0.001) and individual-level ( r ²= 0.54, P < 0.001) corticosterone values, as well as a negative correlation between genetic diversity and cortisol at the individual level ( r ²= 0.17, P = 0.04). No relationship was found between genetic diversity and testosterone ( P = 0.57). The strength of the correlations, especially with corticosterone, suggests potential negative consequences for overall population health, particularly for populations with the lowest genetic diversity.     

Population demography and heterozygosity–fitness correlations in natural guppy populations: An examination using sexually selected fitness traits

Heterozygosity–fitness correlations (HFCs) have been examined in a wide diversity of contexts, and the results are often used to infer the role of inbreeding in natural populations. Although population demography, reflected in population‐level genetic parameters such as allelic diversity or identity disequilibrium, is expected to play a role in the emergence and detectability of HFCs, direct comparisons of variation in HFCs across many populations of the same species, with different genetic histories, are rare. Here, we examined the relationship between individual microsatellite heterozygosity and a range of sexually selected traits in 660 male guppies from 22 natural populations in Trinidad. Similar to previous studies, observed HFCs were weak overall. However, variation in HFCs among populations was high for some traits (although these variances were not statistically different from zero). Population‐level genetic parameters, specifically genetic diversity levels (number of alleles, observed/expected heterozygosity) and measures of identity disequilibrium (g2 and heterozygosity–heterozygosity correlations), were not associated with variation in population‐level HFCs. This latter result indicates that these metrics do not necessarily provide a reliable predictor of HFC effect sizes across populations. Importantly, diversity and identity disequilibrium statistics were not correlated, providing empirical evidence that these metrics capture different essential characteristics of populations. A complex genetic architecture likely underpins multiple fitness traits, including those associated with male fitness, which may have reduced our ability to detect HFCs in guppy populations. Further advances in this field would benefit from additional research to determine the demographic contexts in which HFCs are most likely to occur.     

Estimating genome-wide heterozygosity: effects of demographic history and marker type

Heterozygosity–fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites.     

HERITABILITY OF FITNESS COMPONENTS IN A WILD BIRD POPULATION

Consistently with the prediction that selection should deplete additive genetic variance ( V_A ) in fitness, traits closely associated to fitness have been shown to exhibit low heritabilities ( h ²= V_A /( V_A + V_R )). However, empirical data from the wild indicate that this is in fact due to increased residual variance ( V_R ), rather than due to decreased additive genetic variance, but the studies in this topic are still rare. We investigated relationships between trait heritabilities, additive genetic variances, and traits' contribution to lifetime reproductive success (≈fitness) in a red-billed gull ( Larus novaehollandiae ) population making use of animal model analyses as applied to 15 female and 13 male traits. We found that the traits closely associated with fitness tended to have lower heritabilities than traits less closely associated with fitness. However, in contrast with the results of earlier studies in the wild, the low heritability of the fitness-related traits was not only due to their high residual variance, but also due to their low additive genetic variance. Permanent environment effects—integrating environmental effects experienced in early life as well as nonadditive genetic effects—on many traits were large, but unrelated to traits' importance for fitness.     

Genetic variability and differentiation in Spanish roe deer (Capreolus capreolus): A phylogeographic reassessment within the European framework

Here we study 109 Iberian roe deer individuals corresponding to 9 Spanish populations. Individuals were sampled at locations that are expected to have acted as refugia for the species during the 20th century. Samples were analyzed for a 436 bp mtDNA fragment from the HVI region of mitochondrial DNA and 10 microsatellites. The 109 sequences gave 31 different haplotypes that enabled identification of a new haplogroup (mainly present in Northwestern Iberian populations and representing roughly a third of our samples) that is not present in other European roe deer populations. Using microsatellites, correspondence analysis and molecular coancestry information revealed high molecular differentiation among Northwestern and Central-Southern Spain roe deer populations. Both sequence and microsatellite analysis reveal that the Spanish roe deer populations are genetically heterogeneous and have high genetic structure clearly separating the Pyrenean-reintroduced populations and two main areas for the species in Spain (Northwestern and Central-Southern) coinciding with the two main areas acting as refugia for the majority of the mammal species during glaciations. The implications of the obtained information as regards the phylogeography of the species are discussed together with suggestions as to appropriate strategies for the conservation and management of populations.     

Varying survival of motoneurons and activation of distinct molecular mechanism in response to altered peripheral myelin protein 22 gene dosage

Alteration in the expression level of peripheral myelin protein 22 (PMP22) is the most frequent cause for demyelinating neuropathies of Charcot-Marie-Tooth type. Here, we demonstrate a loss of motoneurons (MNs) in the spinal cords from transgenic mice over-expressing Pmp22 ( Pmp22 ^tg ) while mice lacking Pmp22 [ Pmp22 ^ko ; knockout (ko)] exhibited normal MN numbers at the symptomatic age of 60 days. In order to describe the molecular changes in affected MNs, these cells were isolated from lumbar spinal cords by laser-capture microdissection. Remarkably, the MNs of the Pmp22 ^ko and Pmp22 ^tg mice showed different expression profiles because of the altered Pmp22 expression. The changes in the expression profile of MNs from Pmp22 ^ko mice resemble those described in MNs from mice after nerve injury and included genes that had been described in neuronal growth and regeneration like Gap 43 and Sprr 11a. The changes detected in the expression pattern of MNs from Pmp22 ^tg mice exhibited fewer similarities to other expression patterns. The specific expression pattern in the MNs of the Pmp22 ^ko mice might contribute to the better survival of the MNs. Our study also revealed induction of genes like brain-expressed X-linked 1 ( Bex 1) and desmoplakin ( Dsp ) that had recently been found up-regulated in MNs of human amyotrophic lateral sclerosis patients.     

Properties of the Sodium Extrusion Mechanism Controlled by Nerve Growth Factor in Chick Embryo Dorsal Root Ganglionic Cells

Abstract: Cell dissociates from embryonic chick dorsal root ganglia, incubated for 6 h with ²²Na⁺, accumulated four to six times more radioactivity in the absence than in the presence of Nerve Growth Factor (NGF). The accumulation of radioactivity paralleled the external Na⁺ concentration, indicating that the cells may have been reaching equilibrium with the medium. Delayed presentation of NGF to ²²Na⁺-loaded cells caused a rapid loss of radioactivity, even with extracellular ²²Na⁺ still present, demonstrating that NGF caused an overall efflux of Na⁺ rather than an accelerated equilibration. The Na⁺ exclusion from ²²Na⁺-loaded cells was dependent upon NGF concentration. Use of nutrient-rich medium, serum, and certain hormones and other proteins did not prevent the Na+ accumulation in the absence of NGF or its reversion by delayed NGF administration. Incubation of the ganglionic cells with ouabain or dinitrophenol during the ²²Na⁺ loading period (no NGF) increased the rate, but not the magnitude, of loading. The same incubation carried out in a Na+-free medium and followed by ²²Na⁺ presentation resulted in fast radioactive loading that was identical to that occurring in drug-free, NGF-deprived cells and was not prevented by presentation of NGF together with the ²²Na⁺. These data are consistent with a model in which NGF acts through a Na⁺ pump rather than by restricting Na+ influxes.     

Microsatellite investigation of roe deer (Capreolus capreolus) in Scandinavia reveals genetic differentiation of a Baltic Sea Island population

After a decline in the early 19th century, a remnant population of the Scandinavian roe deer (Capreolus capreolus) was protected in southern Sweden around 1840. The roe deer quickly recovered and recolonized most of the Scandinavian Peninsula. In this study, I analyze microsatellite variation in 14 roe deer populations in Scandinavia to (1) investigate if all Swedish roe deer trace their ancestry to southern Sweden, (2) define other areas where roe deer may have remained during the population decline, and (3) examine if the large geographic distances during the expansion phase have influenced the degree and sorting of genetic variation. The results show that the mainland roe deer most likely trace their ancestry to southern Sweden, but interestingly, the two neighboring populations Övedskloster and Wittskövle in the south are significantly different from each other (p<0.01). Furthermore, the population in Wittskövle and roe deer from Köpingsvik at the Baltic Sea Island Öland are significantly different from all other populations (p<0.1). Thus, potentially, there are more than one founder population that contributed to the current Swedish population. The particular differentiation of roe deer from Öland might be an effect of random population genetic processes during the population expansion phase, potentially in combination with introductions of roe deer from other areas than the Swedish mainland. The results are discussed in relation to management of roe deer in Sweden.     

Rumen Ciliate Protozoa in Ohio White-tailed Deer (Odocoileus virginianus)

ABSTRACT. Rumen contents were obtained from 23 white-tailed deer (Odocoileus virginianus), located in the eastern portion of central Ohio. Samples were taken during late fall and winter over a 4-yr period, 1986–1990. Protozoan numbers ranged from 0.002 to 7.25 × 10⁶ per ml of rumen contents, with a mean of 2.96 × 10⁶. Six deer had protozoan concentrations higher than any values previously reported in ruminants. In all 23 animals, Entodinium dubardi was the only ciliate protozoan species present.     

Specific microsatellite loci for brook charr reveal strong population subdivision on a microgeographic scale

We have isolated specific microsatellite loci from a partial genomic library of brook charr Salvelinus fontinalis. Their usefulness was investigated by measuring intra- and inter-population genetic diversity at four loci among 20 individuals from each of five lakes located 3 to 22 km apart in La Mauricie national park (Canada). These markers were moderately to highly polymorphic. A total of five, six, 16 and 18 alleles per locus were detected, and their overall expected heterozygosity was 0.53, 0.58, 0.86 and 0.87. Strong inter-population diversity was detected. Highly significant differences in allelic frequencies were found in all but two pairwise χ² permutation tests between populations at all loci. Numerous population unique alleles were observed in all five lakes. Consequently, a highly significant component of total genetic diversity was due to interpopulation variance, as exemplified by G _ST values of 0.33, 0.42, 0.47 and 0.84 for each individual locus. Altogether, the results indicated that these loci should be valuable in addressing fine scale population genetics questions in brook charr. To our knowledge, they also represent the first available microsatellites developed in the genus Salvelinus.