Molecular signatures of lineage-specific adaptive evolution in a unique sea basin: the example of an anadromous goby Leucopsarion petersii

Female preferences for male golden snub-nosed monkeys vary with male age and social context

Age is a key factor affecting sexual selection, as many physical and social traits are age-related. Although studies of primate mate choice often consider particular age-related traits, few consider the collective effects of male age. We tested the hypothesis that female golden snub-nosed monkeys Rhinopithecus roxellana prefer prime aged males (10–15 years) over younger and older males. We examined a habituated, provisioned troop during a 3-year study in the Qinling Mountains, China. Prime age males were more likely to be resident males of 1-male units (OMUs) than males of other ages. Since females are free to transfer between OMUs, the number of females per OMU can be indicative of female preferences. We examined the number of females per OMU, and found that it increased with resident male age up to 7–8 years, and declined after 12 years, such that prime age resident males had more females than other resident males. Females also initiated extra-unit copulations with high-ranking prime age males at significantly higher rates than with other males. Nevertheless, females tended to transfer from OMUs with high-ranking, older resident males to those with low-ranking, younger resident males. Thus, females appear to use different strategies when choosing social mates and extra-unit mates (i.e., different social contexts). We speculate that females may perceive early signs of aging in males and trade off the benefits and costs of high rank versus male senescence. This study lays the groundwork for future studies that examine possible direct and indirect benefits of such strategies.

Genomic and phenotypic consequences of two independent secondary contact zones between allopatric lineages of the anadromous ice goby Leucopsarion petersii

Genetic and phenotypic analyses of independent secondary contact zones between certain pairs of divergent populations offer powerful opportunities to assess whether the consequences vary with different environmental backgrounds. Populations of the ice goby Leucopsarion petersii are distributed throughout the Japanese archipelago and comprise genetically and phenotypically divergent groups in the Japan Sea and the Pacific Ocean. In particular, populations in the Japan Sea have a larger body size and numbers of vertebrae than those in the Pacific Ocean. Herein, we performed integrated analyses of genotypes and phenotypes of two independent secondary contact zones and investigated their consequences. Population genetic analyses revealed asymmetric introgression of the mitochondrial genome of either lineage relative to little admixture of nuclear genomes in both secondary contact zones. On phenotype analyses, vertebral numbers were clearly explained by nuclear genomic ancestry in both secondary contact zones, whereas body size was not, suggesting that a little introgression of nuclear genes regulates body size. Actually, we observed biased introgression of a candidate gene, neuropeptide Y (NPY), which potentially controls body size in the ice goby. Moreover, the body size changes in the introgressed populations possibly affect the introgression patterns of mitochondrial genomes across these zones. Collectively, our results demonstrated that genomic and phenotypic consequences of secondary contact varied in marine variable environments.

Phylogeography of the highly invasive sugar beet nematode, Heterodera schachtii (Schmidt, 1871), based on microsatellites

Plant-parasitic nematodes (PPNs) threaten crop production worldwide. Yet few studies have examined their intraspecific genetic diversity or patterns of invasion, critical data for managing the spread of these cryptic pests. The sugar beet nematode Heterodera schachtii, a global invader that parasitizes over 200 plant species, represents a model for addressing important questions about the invasion genetics of PPNs. Here, a phylogeographic study using 15 microsatellite markers was conducted on 231 H. schachtii individuals sampled from four continents, and invasion history was reconstructed through an approximate Bayesian computation approach, with emphasis on the origin of newly discovered populations in Korea. Multiple analyses confirmed the existence of cryptic lineages within this species, with the Korean populations comprising one group (group 1) and the populations from Europe, Australia, North America, and western Asia comprising another (group 2). No multilocus genotypes were shared between the two groups, and large genetic distance was inferred between them. Population subdivision was also revealed among the populations of group 2 in both population comparison and STRUCTURE analyses, mostly due to different divergent times between invasive and source populations. The Korean populations showed substantial genetic homogeneity and likely originated from a single invasion event. However, none of the other studied populations were implicated as the source. Further studies with additional populations are needed to better describe the distribution of the potential source population for the East Asian lineage.

Molecular biology and functional genomics of immune-endocrine interactions in the Japanese eel, Anguilla japonica

Immune-endocrine interactions are an important pathogen resistance mechanism in fish. We review the immune-endocrine interactions in the Japanese eel, Anguilla japonica, with special reference to high throughput gene sequencing. These data may be relevant to the significant decrease in the eel harvest in recent years and will aid in the selection of appropriate disease-resistant strains for aquaculture. More than 1000 sequences that whose expression in elvers responded to air exposure were identified through comprehensive gene expression analysis using next-generation sequencing. These included transcription factors within the MAPK pathway. Significant changes in expression after air exposure were detected by quantitative polymerase chain reaction analysis in many genes related to disease resistance. These factors include innate immune system factors and cytokines that interact with the endocrine system during the stress response. Other applications of immune-endocrine interactions in eel culture are discussed.

Estimating Relatedness in the Presence of Null Alleles

Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set.