Journal of Heredity最新文献

Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: 1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? 2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? 3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? 4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.

Facultative parthenogenesis (FP), or asexual reproduction by sexually-reproducing female animals, has been reported across several clades of vertebrates and is increasingly being recognized as a reproductive mechanism with significant implications for the genetic variation of captive and wild populations. The definitive identification of parthenogens requires molecular confirmation, with large genomic data sets necessary to accurately parse the parthenogenetic mechanism (i.e., endoduplication, gametic duplication, terminal fusion automixis, or central fusion automixis). Current methods for inferring FP from large genomic data sets are statistically intensive, require competency in R scripting for their execution, and are not designed for detection of facultative parthenogenesis or screening of large numbers of mother/offspring pairs, whereas small data sets (i.e., microsatellites) that can be evaluated visually lack the power to discriminate among FP mechanisms. Here, we present the user-friendly software program, ParthenoGenius, that uses intuitive logic to infer presence and mechanism of FP from even large genomic data sets comprising many mothers and offspring. ParthenoGenius runs relatively quickly and does not require the researcher to have knowledge of R scripting or statistics. ParthenoGenius was tested on eight empirical data sets, and in each case identified parthenogens (and parthenogenic mechanism when present) consistent with results of previous studies or corroborating evidence. ParthenoGenius will facilitate the rapid screening of large genomic data sets comprising many mothers and offspring for the presence and mechanism of parthenogenesis, improving our understanding of the frequency and phylogenetic distribution of FP across the animal kingdom.

Scorpions are an ancient and charismatic group of arthropods with medical importance, but a high-quality reference genome for this group is still lacking. Here we perform whole-genome sequencing of Mesobuthus przewalskii, a desert scorpion endemic to the Taklimakan Desert. We combine PacBio HiFi sequencing and Hi-C chromosome conformation capturing to generate chromosomal-level, haplotype-resolved, and fully annotated genome assembly for this medically important scorpion. The assembly consists of two haplotypes (1052.01 Mbp and 1055.19 Mbp, respectively) reaching chromosome-level contiguity and >98% BUSCO completeness. Sequences were anchored in 13 chromosomes with a contig N50 of 34.44 Mbp and scaffold N50 of 81.43 Mbp. Several key genome features and the mitochondrial genome assembly were also provided. This genome represents the fifth but the most complete assembly for the order Scorpiones.

Sex chromosomes often differ between closely related species and can even be polymorphic within populations. Species with multifactorial sex determination segregate for multiple different sex determining loci within populations, making them uniquely informative of the selection pressures that drive the evolution of sex chromosomes. The house fly (Musca domestica) is a model species for studying multifactorial sex determination because male determining genes have been identified on all six of the chromosomes, which means that any chromosome can be a "proto-Y". Natural populations of house fly also segregate for a recently derived female-determining locus, meaning house flies also have a proto-W chromosome. The different proto-Y chromosomes are distributed along latitudinal clines on multiple continents, their distributions can be explained by seasonality in temperature, and they have temperature-dependent effects on physiological and behavioral traits. It is not clear, however, how the clinal distributions interact with the effect of seasonality on the frequencies of house fly proto-Y and proto-W chromosomes across populations. To address this question, we measured the frequencies of house fly proto-Y and proto-W chromosomes across nine populations in the United States of America. We confirmed the clinal distribution along the eastern coast of North America, but it is limited to the eastern coast. In contrast, annual mean daily temperature range predicts proto-Y chromosome frequencies across the entire continent. Our results therefore suggest that temperature heterogeneity can explain the distributions of house fly proto-Y chromosomes in a way that does not depend on the cline.

This study evaluated the effectiveness of genetic introgression of the SLICK1 allele derived from Senepol cattle into the Holstein breed to enhance thermotolerance. The SLICK1 allele, located in PRLR gene, confers a short and sleek coat that is inherited as a simple dominant phenotype. Approximately 40 years ago, the University of Florida initiated efforts to introgress this allele into the Holstein population. Here we tracked the introgression of the SLICK1 allele using a medium-density genotyping array and a reference population of both breeds (50 Holstein, 46 Senepol). Among the 31 SLICK1+ Holsteins, there was 15.25% ± 11.11% (mean ± SD) Senepol ancestry on BTA20. Holsteins at the University of Florida descended from slick matings that did not inherit the SLICK1 allele (n=9) exhibited no Senepol ancestry. A secondary introgression of Senepol genetics in SLICK1+ animals was found on BTA4, spanning 54 markers and 15 genes, with 26.67% Senepol ancestry. This region, previously linked to heat stress adaptation, suggests that the introgression extends beyond the SLICK1 allele to incorporate additional beneficial genetics for thermal stress adaptation. These findings indicate that deliberate introgression of the SLICK1 allele enhances specific traits and potentially introduces other adaptive genetic variations. The study demonstrates the successful use of genetic interventions to improve livestock resilience against environmental challenges without significantly disrupting the recipient breed's genetic structure. The introgression of the SLICK1 allele serves as a model for breeding programs aimed at optimizing animal welfare and productivity in the face of global climate change while maintaining breed integrity.

Anthropogenically fragmented populations may have reduced fitness due to loss of genetic diversity and inbreeding. The extent of such fitness losses due to fragmentation and potential gains from conservation actions are infrequently assessed together empirically. Controlled crosses within and among populations can identify whether populations are at risk of inbreeding depression and whether interpopulation crossing alleviates fitness loss. Because fitness depends on environment and life stage, studies quantifying cumulative fitness over a large portion of the lifecycle in conditions that mimic natural environments are most informative. To assess fitness consequences of habitat fragmentation, we leveraged controlled within-family, within-population, and between-population crosses to quantify inbreeding depression and heterosis in seven populations of Echinacea angustifolia within a 6400-hectare area. We then assessed cumulative offspring fitness after 14 years of growth in a natural experimental plot (N = 1136). Mean fitness of progeny from within-population crosses varied considerably, indicating genetic differentiation among source populations, even though these sites are all less than 9 km apart. The fitness consequences of within-family and between-population crosses varied in magnitude and direction. Only one of the seven populations showed inbreeding depression of high effect, while four populations showed substantial heterosis. Outbreeding depression was rare and slight. Our findings indicate that local crossings between isolated populations yield unpredictable fitness consequences ranging from slight decreases to substantial increases. Interestingly, inbreeding depression and heterosis did not relate closely to population size, suggesting that all fragmented populations could contribute to conservation goals as either pollen recipients or donors.

The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980Mb E. newberryi reference genome has an N50 of 34Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the northern tidewater goby, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.

Squamate reptiles are a highly diverse and intriguing group of tetrapods, offering valuable insights into the evolution of amniotes. The Australian water dragon (Intellagama lesueurii) is a member of the Agamidae, and sister to the core mesic Australian endemic radiation (Amphibolurinae). The species is renowned for its urban adaptability and complex social systems. We report a 1.8 Gb chromosome-length genome assembly together with the annotation of 23,675 protein-coding genes. Comparative analysis with other squamate genomes highlights gene family expansions associated with immune function, energetic homeostasis, and wound healing. This reference genome will serve as a valuable resource for studies of evolution and environmental resilience in lizards.

The African hunting dog (Lycaon pictus, 2n=78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure as well as interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome level assembly of an African hunting dog. Assembled according to VGP guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36 % of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO analysis showed 95.4 % completeness based on Сarnivora conservative genes (carnivora_odb10). When compared to other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the 1st and 3rd depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.