Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent

Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are “intrinsic,” meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse—albeit indirect—signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.

Molecular species delimitation refines the taxonomy of native and nonnative physinine snails in North America

Being able to associate an organism with a scientific name is fundamental to our understanding of its conservation status, ecology, and evolutionary history. Gastropods in the subfamily Physinae have been especially troublesome to identify because morphological variation can be unrelated to interspecific differences and there have been widespread introductions of an unknown number of species, which has led to a speculative taxonomy. To resolve uncertainty about species diversity in North America, we targeted an array of single-locus species delimitation methods at publically available specimens and new specimens collected from the Snake River basin, USA to generate species hypotheses, corroborated using nuclear analyses of the newly collected specimens. A total-evidence approach delineated 18 candidate species, revealing cryptic diversity within recognized taxa and a lack of support for other named taxa. Hypotheses regarding certain local endemics were confirmed, as were widespread introductions, including of an undescribed taxon likely belonging to a separate genus in southeastern Idaho for which the closest relatives are in southeast Asia. Overall, single-locus species delimitation was an effective first step toward understanding the diversity and distribution of species in Physinae and to guiding future investigation sampling and analyses of species hypotheses.

Four New Species of Hemileccinum (Xerocomoideae, Boletaceae) from Southwestern China

The genus Hemileccinum belongs to the subfamily Xerocomoideae of the family Boletaceae. In this study, phylogenetic inferences of Hemileccinum based on sequences of a single-locus (ITS) and a multi-locus (nrLSU, tef1-α, rpb1, rpb2) were conducted. Four new species, namely H. abidum, H. brevisporum, H. ferrugineipes and H. parvum were delimited and proposed based on morphological and molecular evidence. Descriptions and line-drawings of them were presented, as well as their comparisons to allied taxa. Our study shed new light on the recognition of the genus. The pileipellis of the species in this genus should mostly be regarded as (sub)epithelium to hyphoepithelium, because the pileipellis of most studied species here is composed of short inflated cells in the inner layer (subpellis) and filamentous hyphae in outer layer (suprapellis). The basidiospores of the studied species, including the type species, H. impolitum, have a warty surface.

Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs

Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.

Making the most of potential: potential games and genotypic convergence

We consider genotypic convergence of populations and show that under fixed fitness asexual and haploid sexual populations attain monomorphic convergence (even under genetic linkage between loci) to basins of attraction with locally exponential convergence rates; the same convergence obtains in single locus diploid sexual reproduction but to polymorphic populations. Furthermore, we show that there is a unified theory underlying these convergences: all of them can be interpreted as instantiations of players in a potential game implementing a multiplicative weights updating algorithm to converge to equilibrium, making use of the Baum–Eagon Theorem. To analyse varying environments, we introduce the concept of ‘virtual convergence’, under which, even if fixation is not attained, the population nevertheless achieves the fitness growth rate it would have had under convergence to an optimal genotype. Virtual convergence is attained by asexual, haploid sexual and multi-locus diploid reproducing populations, even if environments vary arbitrarily. We also study conditions for true monomorphic convergence in asexually reproducing populations in varying environments.

A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles ‘GGG’ for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.

Eagle for better genome-wide association mapping

Eagle is an R package for multi-locus association mapping on a genome-wide scale. It is unlike other multi-locus packages in that it is easy-to-use for R users and non-users alike. It has two modes of use, command line and GUI. Eagle is fully documented and has its own supporting website, http://eagle.r-forge.r-project.org/index.html. Eagle is a significant improvement over the method-of-choice, single-locus association mapping. It has greater power to detect SNP-trait associations. It is based on model selection, linear mixed models, and a clever idea on how random effects can be used to identify SNP-trait associations. Through an example with real mouse data, we demonstrate Eagle’s ability to bring clarity and increased insight to single-locus findings. Initially, we see Eagle complementing single-locus analyses. However, over time, we hope the community will make, increasingly, multi-locus association mapping their method-of-choice for the analysis of genome-wide association study data.

ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta

Together with local chromatin structure, gene accessibility, and the presence of transcription factors, gene positioning is implicated in gene expression regulation. Although the basic mechanisms are expected to be conserved in eukaryotes, less is known about the role of gene positioning in plant cells, mainly due to the lack of a highly resolutive approach. In this study, we adapted the use of the ANCHOR system to perform real-time single locus detection in planta. ANCHOR is a DNA-labeling tool derived from the chromosome partitioning system found in many bacterial species. We demonstrated its suitability to monitor a single locus in planta and used this approach to track chromatin mobility during cell differentiation in Arabidopsis thaliana root epidermal cells. Finally, we discussed the potential of this approach to investigate the role of gene positioning during transcription and DNA repair in plants.

Genetic evidence for environment-dependent hybrid incompatibilities in threespine stickleback

Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are 'intrinsic', meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (semi-natural experimental ponds) or the laboratory (aquaria). We tested for differences in excess heterozygosity between these two environments at ancestry informative loci—a genetic signature of selection against incompatibilities. We found that excess ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Previous results from F1 hybrids in the field suggest that pond-specific (single-locus) heterosis is unlikely to explain this finding. Our study suggests that, in stickleback, a coarse signal of environment-dependent hybrid incompatibilities is reliably detectable and that extrinsic incompatibilities have evolved before intrinsic incompatibilities.

New Simple Sequence Repeat Markers on Linkage Groups 2 and 7, and Investigation of New Sources of Eastern Filbert Blight Resistance in Hazelnut

Eastern filbert blight (EFB), caused by Anisogramma anomala, is a fungal disease threatening the european hazelnut (Corylus avellana) industry in the Willamette Valley of Oregon. The pathogen is endemic to the eastern United States where it causes little damage to the wild Corylus americana but causes severe cankers on most cultivars of the commercially important european hazelnut. The host genetic resistance in ‘Gasaway’ is conferred by a dominant allele at a single locus on linkage group 6 (LG6), and resistance from several other sources has been mapped to the same region. Some fungal isolates can overcome ‘Gasaway’ resistance, prompting a search for other sources of resistance. Resistance from other sources has been mapped to LG2 and LG7, for which additional simple sequence repeat (SSR) markers would facilitate marker-assisted selection (MAS). In this study, an in silico approach was used to develop new polymorphic SSR markers in the EFB resistance regions on LG2 and LG7. Starting with a search of 17 contigs of the ‘Jefferson’ genome sequence, 45 new polymorphic SSR markers were developed, characterized, and placed on the linkage map. The new SSR markers had an average of 10.18 alleles per locus, and average values for expected heterozygosity, observed heterozygosity, polymorphism information content, and frequency of null alleles of 0.72, 0.65, 0.68, and 0.068, respectively. Of the 42 new polymorphic SSRs segregating in the mapping population, 24 were on LG2, 12 were on LG7, and six were placed on other LGs. The new and previously developed SSR markers were used to study six new sources of EFB resistance, four from Russia and two from Crimea. Six resistant selections were crossed with susceptible selections, resulting in 7 progenies. Phenotyping for disease response revealed that segregation in progenies of the two Moscow selections (#2 and #27), one Russian selection (OSU 1187.101), and one Crimean selection (H3R12P62) fit the 1:1 segregation ratio expected for control of resistance by a dominant allele at a single locus; but in progenies of the other Russian selection (OSU 1166.123) and the other Crimean selection (H3R07P11), there was an excess of resistant seedlings. Correlation of disease scores and alleles at SSR loci indicated that resistance from three Russian selections (Moscow selections #2 and #27 and OSU 1166.123) and the Crimean selection H3R12P62 was on LG7, while resistance from Russian selection OSU 1187.101 was on LG2. Resistance from Crimean selection H3R07P11 was not correlated with markers on LG6, or LG2, or LG7. These sources and new SSR markers will be useful in MAS and the pyramiding of resistance genes in the breeding of new EFB-resistant cultivars.