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According to the revisionist interpretation of Mendel's pea crosses, his primary aim was not to study the inheritance of traits. Instead, he was interested in the question raised by Linnaeus as to whether new species could arise from the hybridization of existing species. The genetic interpretation is therefore seen as ahistorical by the revisionists. This view goes back to the 1979 article "Mendel no Mendelian?" by the historian of science R.C. Olby. A closer analysis shows that Olby implicitly assumed Mendel adhered to the unusual strictest species definition for Pisum. However, we argue that Mendel only mentions the hypothetical application of this strict definition in his 1866 paper. Like most of his contemporaries, Mendel accepted variation within species where the differences between varieties and species were a matter of degree. After researching variable hybrids in peas (Pisum; 1854-1863), Mendel also studied constant hybrids in hawkweeds (Hieracium; 1866-1873), which he considered to be new species. There is no debate about the latter, but the matter becomes muddled because Olby lumps Pisum and Hieracium together, despite their having completely different reproduction systems. Based on newly discovered historical sources, we also dispute several other assumptions made by Olby. We do not consider Olby's claim that Mendel conducted the Pisum experiments to investigate species multiplication to be tenable., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Distinctly different electrophoretic patterns of red cell glucose-6-phosphate dehydrogenase were resolved from the hemolyzates of horse and donkey erythrocytes. Examination of their reciprocal hybrids, mules and hinnies, showed that the red cells of female mules and female hinnies contain both horse and donkey G-6-PD; the male mule with an X chromosome from its horse mother contained pure horse G-6-PD, whereas the male hinny with the donkey X chromosome contained pure donkey G-6-PD. These findings on the male reciprocal hybrids suggest X-linkage.

A study of the immunological properties of phage strains derived from T2 x T6 crosses revealed that the majority of the progeny differ serologically from the parental viruses. Some hybrids were found to contain head membranes having the serological specificity of both T2 and T6 phages, while others contained tail sheaths of the former and the tail fibers of the latter. Since the immunological properties of all hybrids were heritable, it has been concluded that the serological specificity of the head proteins of T2 and T6 is controlled by at least two genetic determinants, and that the specificities of the fiber and sheath proteins may be governed by single genes. Furthermore it was found that nucleic acids of hybrids had similar proportions of unsubstituted, mono- and diglucosylated hydroxymethylcytosine nucleotides to the nucleic acid of either T2 or T6 phage. Since the parental and hybrid viruses having chemically similar nucleic acids contained in some instances serologically different proteins, it has also been concluded that the extent of glucosylation of the hydroxymethylcytosine component of viral nucleic acids and the immunological properties of viral proteins are independently heritable traits of T2 and T6 bacteriophages.

Segregation distorters (SDs) are genetic elements that distort the Mendelian segregation ratio to favor their own transmission and are able to spread even when they incur fitness costs on organisms carrying them. Depending on the biology of the host organisms and the genetic architecture of the SDs, the population dynamics of SDs can be highly variable. Inbreeding is considered an effective mechanism for inhibiting the spread of SDs in populations, and can evolve as a defense mechanism against SDs in some systems. However, we show that inbreeding in the form of selfing in fact promotes the spread of SDs acting as pollen killers in a toxin-antidote system in hermaphroditic plants by two mechanisms: (i) By reducing the effective recombination rate between killer and antidote loci in the two-locus system and (ii) by increasing the proportion of SD alleles in individual flowers, rather than in the general gene-pool. We also show that in rice (Oryza sativa L.), a typical hermaphroditic plant, all molecularly characterized SDs associated with pollen killing were involved in population hybridization and have introgressed across different species. Paradoxically, these loci, which are associated with hybrid incompatibility and can be thought of as Bateson-Dobzhansky-Muller incompatibility loci are expected to reduce gene-flow between species, in fact cross species boundaries more frequently than random loci, and may act as important drivers of introgression.

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on the Discrete Wavelet Transform to study the genomic scale of local ancestry variation and its association with recombination rates and show that these methods capture temporal dynamics of drift and genome-wide selection after hybridization. We apply these methods to published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio) and to inferred Neanderthal introgression in modern humans. Across systems, upward of 20% of variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. Signatures of selection at fine genomic scales suggest selection over longer time scales; however, we suggest that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from contiguous segments of genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available and can help shed light on generalities of the genomic consequences of interspecific hybridization.

Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].

Coevolved genetic interactions within populations can be disrupted by hybridization resulting in loss of fitness in hybrid individuals (i.e., hybrid breakdown). However, the extent to which variation in fitness-related traits among hybrids is inherited across generations remains unclear, and variation in these traits may be sex-specific in hybrids due to differential effects of genetic incompatibilities in females and males. Here we present two experiments investigating variation in developmental rate among reciprocal interpopulation hybrids of the intertidal copepod Tigriopus californicus. Developmental rate is a fitness-related trait in this species that is affected by interactions between mitochondrial-encoded and nuclear-encoded genes in hybrids that result in variation in mitochondrial ATP synthesis capacities. First, we show that F2 -hybrid developmental rate is equivalent in two reciprocal crosses and is unaffected by sex, suggesting that breakdown of developmental rate is likely experienced equally by females and males. Second, we demonstrate that variation in developmental rate among F3 hybrids is heritable; times to copepodid metamorphosis of F4 offspring of fast-developing F3 parents (12.25 ± 0.05 days, μ ± SEM) were significantly faster than those of F4 offspring of slow-developing parents (14.58 ± 0.05 days). Third, we find that ATP synthesis rates in these F4 hybrids are unaffected by the developmental rates of their parents, but that mitochondria from females synthesize ATP at faster rates than mitochondria from males. Taken together, these results suggest that sex-specific effects vary among fitness-related traits in these hybrids, and that effects likely associated with hybrid breakdown display substantial inheritance across hybrid generations.

Understanding relationships among warming climate, increased drought severity, and the genetic architecture of hybrid drought resilience is necessary for forest conservation and management. We calculated three drought-related tree-ring-growth indices (dendrophenotypes) using tree-ring data from hybrid Pinus strobiformis–Pinus flexilis study trees at nine sites across Colorado, New Mexico, Arizona, and Texas. Along with hybrid index (percentage of P. strobiformis ancestry inherited by a single tree) and climate variables, we used dendrophenotypes to (Q1) examine relationships among climate and hybrid index, (Q2) examine relationships between dendrophenotypes and hybrid index, and (Q3) conduct a genotype–phenotype analysis. We observed a significant correlation between hybrid index and dendrophenotypes resulting from high-temperature drought in addition to a significant correlation between those dendrophenotypes and our dataset of single-nucleotide polymorphisms. We conclude that P. strobiformis–P. flexilis trees exhibiting higher hybrid indices are more resilient to high-temperature drought events and encourage future research that identifies a genetic linkage between relevant loci and their conferred physiological benefits. [ABSTRACT FROM AUTHOR]

Sterility among hybrids is one of the most prevalent forms of reproductive isolation delineating species boundaries and is expressed disproportionately in heterogametic XY males. While hybrid male sterility (HMS) due to the "large X effect" is a well-recognized mechanism of reproductive isolation, it is less clear how HMS manifests in species that lack heteromorphic sex chromosomes. We evaluated differences in allele frequencies at approximately 460,000 SNPs between fertile and sterile F2 interpopulation male hybrids to characterize the genomic architecture of HMS in a species without sex chromosomes (Tigriopus californicus). We tested associations between HMS and mitochondrial-nuclear and/or nuclear-nuclear signatures of incompatibility. Genomic regions associated with HMS were concentrated on a single chromosome with the same primary 2-Mbp regions identified in one pair of reciprocal crosses. Gene Ontology analysis revealed that annotations associated with spermatogenesis were the most overrepresented within the implicated region, with nine protein-coding genes connected with this process found in the quantitative trait locus of chromosome 2. Our results indicate that a narrow genomic region was associated with the sterility of male hybrids in T. californicus and suggest that incompatibilities among select nuclear loci may replace the large X effect when sex chromosomes are absent.

In 2022, field investigation was conducted to examine the genetic diversity among 30 pink brinjal (eggplant, Solanum melongena L.) genotypes originating from India. Mahalanobis D2 analysis was performed to analyze the data for eighteen growth, yield and quality characters. Among the traits examined, the total fruit yield per plant made the most significant contribution towards diversity. Thirty genotypes were meaningfully grouped into eight clusters. Cluster I, the largest, had eight genotypes, followed by Cluster II and Cluster IV. There was no direct correlation observed between the geographical distribution and genetic divergence. Among all clusters formed, Cluster VII exhibited maximum intra-cluster distance followed by Cluster VI. Observing the inter-cluster distances, the maximum divergence was noted between Cluster III and Cluster IV suggesting that genotypes within these clusters could serve as valuable parents for hybridization programmes aimed at producing highly heterotic hybrids and identifying transgressive segregants in the F2 generation.