scholarly journals The Genome of the Margined White Butterfly (Pieris macdunnoughii): Sex Chromosome Insights and the Power of Polishing with PoolSeq Data

2021 ◽  
Vol 13 (4) ◽  
Author(s):  
Rachel A Steward ◽  
Yu Okamura ◽  
Carol L Boggs ◽  
Heiko Vogel ◽  
Christopher W Wheat
Keyword(s):  
North American ◽  
Sex Chromosome ◽  
Egg Laying ◽  
Future Research ◽  
Z Chromosome ◽  
Fusion Event ◽  
Evolutionary Trap ◽  
Comparable Performance ◽  
Insect Interactions ◽  
Chromosome Level

Abstract We report a chromosome-level assembly for Pieris macdunnoughii, a North American butterfly whose involvement in an evolutionary trap imposed by an invasive Eurasian mustard has made it an emerging model system for studying maladaptation in plant–insect interactions. Assembled using nearly 100× coverage of Oxford Nanopore long reads, the contig-level assembly comprised 106 contigs totaling 316,549,294 bases, with an N50 of 5.2 Mb. We polished the assembly with PoolSeq Illumina short-read data, demonstrating for the first time the comparable performance of individual and pooled short reads as polishing data sets. Extensive synteny between the reported contig-level assembly and a published, chromosome-level assembly of the European butterfly Pieris napi allowed us to generate a pseudochromosomal assembly of 47 contigs, placing 91.1% of our 317 Mb genome into a chromosomal framework. Additionally, we found support for a Z chromosome arrangement in P. napi, showing that the fusion event leading to this rearrangement predates the split between European and North American lineages of Pieris butterflies. This genome assembly and its functional annotation lay the groundwork for future research into the genetic basis of adaptive and maladaptive egg-laying behavior by P. macdunnoughii, contributing to our understanding of the susceptibility and responses of insects to evolutionary traps.

scholarly journals Chromosomal Analysis in Crotophaga ani (Aves, Cuculiformes) Reveals Extensive Genomic Reorganization and an Unusual Z-Autosome Robertsonian Translocation

Cells ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Rafael Kretschmer ◽  
Ricardo José Gunski ◽  
Analía del Valle Garnero ◽  
Thales Renato Ochotorena de Freitas ◽  
Gustavo Akira Toma ◽  
...  
Keyword(s):  
Robertsonian Translocation ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Rare Event ◽  
Chromosome Morphology ◽  
Z Chromosome ◽  
Molecular Cytogenetic ◽  
Intrachromosomal Rearrangements ◽  
Genomic Reorganization

Although cytogenetics studies in cuckoos (Aves, Cuculiformes) have demonstrated an interesting karyotype variation, such as variations in the chromosome morphology and diploid number, their chromosome organization and evolution, and relation with other birds are poorly understood. Hence, we combined conventional and molecular cytogenetic approaches to investigate chromosome homologies between chicken and the smooth-billed ani (Crotophaga ani). Our results demonstrate extensive chromosome reorganization in C. ani, with interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were observed in some macrochromosomes, including the Z chromosome. The most evolutionary notable finding was a Robertsonian translocation between the microchromosome 17 and the Z chromosome, a rare event in birds. Additionally, the simple short repeats (SSRs) tested here were preferentially accumulated in the microchromosomes and in the Z and W chromosomes, showing no relationship with the constitutive heterochromatin regions, except in the W chromosome. Taken together, our results suggest that the avian sex chromosome is more complex than previously postulated and revealed the role of microchromosomes in the avian sex chromosome evolution, especially cuckoos.

VIEWPOINT. An hypothesis to explain the linkage between kakapo (Strigops habroptilus) breeding and the mast fruiting of their food trees

2008 ◽  
Vol 35 (1) ◽  
pp. 1 ◽  
Author(s):  
Andrew E. Fidler ◽  
Stephen B. Lawrence ◽  
Kenneth P. McNatty
Keyword(s):  
Egg Yolk ◽  
Ovarian Follicles ◽  
Yolk Protein ◽  
Egg Laying ◽  
Food Plants ◽  
Mast Seeding ◽  
Future Research ◽  
Yolk Protein Genes ◽  
Hypothetical Mechanism ◽  
Future Research Directions

An important goal in the intensive conservation management of New Zealand’s critically endangered nocturnal parrot, kakapo (Strigops habroptilus), is to increase the frequency of breeding attempts. Kakapo breeding does not occur annually but rather correlates with 3–5-year cycles in ‘mast’ seeding/fruiting of kakapo food plants, most notably podocarps such as rimu (Dacrydium cupressinum). Here we advance a hypothetical mechanism for the linking of kakapo breeding with such ‘mast’ seeding/fruiting. The essence of the hypothesis is that exposure to low levels of dietary phytochemicals may, in combination with hepatic gene ‘memory’, sensitise egg yolk protein genes, expressed in female kakapo livers, to oestrogens derived from developing ovarian follicles. Only in those years when the egg yolk protein genes have been sufficiently ‘pre-sensitised’ by dietary chemicals do kakapo ovarian follicles develop to ovulation and egg-laying occurs. While speculative, this hypothesis is both physiologically and evolutionarily plausible and suggests both future research directions and relatively simple interventions that may afford conservation workers some influence over kakapo breeding frequency.

scholarly journals From individual to population level: Temperature and snow cover modulate fledging success through breeding phenology in greylag geese (Anser anser)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Didone Frigerio ◽  
Petra Sumasgutner ◽  
Kurt Kotrschal ◽  
Sonia Kleindorfer ◽  
Josef Hemetsberger
Keyword(s):  
Ambient Temperature ◽  
Reproductive Output ◽  
Population Level ◽  
Egg Laying ◽  
Future Research ◽  
Breeding Phenology ◽  
Anser Anser ◽  
Fledging Success ◽  
Average Annual Temperature ◽  
Greylag Geese

AbstractLocal weather conditions may be used as environmental cues by animals to optimize their breeding behaviour, and could be affected by climate change. We measured associations between climate, breeding phenology, and reproductive output in greylag geese (Anser anser) across 29 years (1990–2018). The birds are individually marked, which allows accurate long-term monitoring of life-history parameters for all pairs within the flock. We had three aims: (1) identify climate patterns at a local scale in Upper Austria, (2) measure the association between climate and greylag goose breeding phenology, and (3) measure the relationship between climate and both clutch size and fledging success. Ambient temperature increased 2 °C across the 29-years study period, and higher winter temperature was associated with earlier onset of egg-laying. Using the hatch-fledge ratio, average annual temperature was the strongest predictor for the proportion of fledged goslings per season. There is evidence for an optimum time window for egg-laying (the earliest and latest eggs laid had the lowest fledging success). These findings broaden our understanding of environmental effects and population-level shifts which could be associated with increased ambient temperature and can thus inform future research about the ecological consequences of climate changes and reproductive output in avian systems.

Evaluation of Four Methods to Identify the Homozygotic Sex Chromosome in Small Populations

2021 ◽  
Author(s):  
Charles Christian Riis Hansen ◽  
Kristen M. Westfall ◽  
Snaebjörn Pálsson
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Read Depth ◽  
Mapping Method ◽  
Small Population ◽  
Genomic Variation ◽  
Z Chromosome ◽  
Effective Population ◽  
Organelle Genomes ◽  
Heterogametic Sex

Abstract BackgroundWhole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types differ in effective population size and can have highly disparate evolutionary histories, it is imperative to take this information into account when analysing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome in a small population using two whole genome sequences (WGS) and 133 RAD sequences of white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold in a male and a female, ii) heterozygosity per scaffold in a male and a female, iii) mapping to a reference genome of a related species (chicken) with identified sex chromosomes, and iv) analysis of SNP-loadings from a principal components analysis (PCA), based on the low-depth RADseq data. ResultsThe best performing approach was the reference mapping (method iii), which identified 98.12% of the expected homogametic sex chromosome (Z). The read depth per scaffold (method i) identified 86.41% of the homogametic sex chromosome with few false positives. The SNP-loading scores (method iv) found 78.6% of the Z-chromosome and had a false positive discovery rate of more than 10%. The heterozygosity per scaffold (method ii) did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W). The evaluation of these methods also revealed 10 Mb of likely PAR and gametologous regions.ConclusionIdentification of the homogametic sex chromosome in a small population is best accomplished by reference mapping or examining read depth differences between sexes.

scholarly journals Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides)

2021 ◽  
Author(s):  
Anne-Laure Ferchaud ◽  
Claire Mérot ◽  
Eric Normandeau ◽  
Jiannis Ragoussis ◽  
Charles Babin ◽  
...  
Keyword(s):  
Sex Determination ◽  
Single Molecule ◽  
Sex Chromosome ◽  
Whole Genome Sequence ◽  
Greenland Halibut ◽  
Syntenic Relationship ◽  
Greenland Halibut Reinhardtius Hippoglossoides ◽  
Reinhardtius Hippoglossoides ◽  
Sex Determination System ◽  
Chromosome Level

Abstract Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that, similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex-determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.

Conclusion

2020 ◽  
pp. 251-260
Author(s):  
Frank Towers
Keyword(s):  
Nineteenth Century ◽  
North American ◽  
American History ◽  
Comparative Studies ◽  
Future Research ◽  
Nation State ◽  
Research Questions ◽  
National Framework

Whereas the introduction to this volume focused on the question of sovereignty and the nation-state, our conclusion takes stock of another important theme of this volume, writing North American history outside of a national framework. Riding the crest of a wave of studies on transnational and global comparative studies of the nineteenth century, historians working in this field would do well to pause briefly to take stock of its achievements, limitations, and future research questions....

scholarly journals Worldwide Feeding Host Plants of Spotted Lanternfly, With Significant Additions From North America

2020 ◽  
Vol 49 (5) ◽  
pp. 999-1011 ◽  
Author(s):  
Lawrence Barringer ◽  
Claire M Ciafré
Keyword(s):  
North America ◽  
Host Plant ◽  
North American ◽  
Host Plants ◽  
Egg Laying ◽  
Potential Range ◽  
Feeding Behaviors ◽  
Invasive Insect ◽  
Tree Of Heaven ◽  
Host Plant Use

Abstract The spotted lanternfly Lycorma delicatula (White) is an invasive insect spreading throughout southeast Asia and eastern North America. The rapid spread of this species is facilitated by the prevalence of its preferred host, tree of heaven (Ailanthus altissima (Mill.) Swingle), as well as its use of many other host plants. While the spotted lanternfly has been previously reported to use over 65 plant species, most of these reports are from Asia and may not be applicable in North America. Additionally, many of the known hosts have not been specified as feeding hosts or as egg laying substrates. To better understand the potential impacts of this invasive insect on natural and cultivated systems in North America, we reviewed records from published and unpublished results and observations of host plant use by spotted lanternfly. We aggregated 172 host plant records worldwide and found feeding behaviors associated with 103 plant taxa across 33 families and 17 orders, 20 of which were not previously known to be associated with SLF and 15 of which were not confirmed as feeding hosts. North American records account for 56 of these taxa which include native, cultivated, and nonnative species. As a result, the spotted lanternfly has the potential to impact a wide assortment of ecosystems throughout its potential range and its North American distribution may not be limited by the presence of tree of heaven.

scholarly journals Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds

2019 ◽  
Vol 11 (8) ◽  
pp. 2376-2390 ◽  
Author(s):  
Luohao Xu ◽  
Simon Yung Wa Sin ◽  
Phil Grayson ◽  
Scott V Edwards ◽  
Timothy B Sackton
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary Dynamics ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Z Chromosome ◽  
Recombination Suppression ◽  
Evolutionary Forces ◽  
Genomic Level ◽  
Standard Models ◽  
Pseudoautosomal Regions

Abstract Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.

scholarly journals Distribution Matters: Feminist Bookstores as Cultural Interaction Spaces

2018 ◽  
Vol 13 (1) ◽  
pp. 57-75
Author(s):  
Kathy Liddle
Keyword(s):  
Identity Formation ◽  
North American ◽  
Physical Space ◽  
Interaction Space ◽  
Future Research ◽  
Audience Reception ◽  
Cultural Interaction ◽  
Historical Case ◽  
Group Solidarity ◽  
Cultural Objects

To investigate the historical case of North American feminist bookstores, I use archival materials, interviews, and surveys to consider how cultural distribution sites affect the acquisition and interpretation of cultural objects. The findings point to the importance and variety of distributor conditions, including physical space, atmosphere, bookseller characteristics, stock, and audience members. I develop the concept of the cultural interaction space, defined as a location where a distributor, its cultural objects, and its audience converge. These spaces provide opportunities for interaction, observation, and experimentation with both tangible and intangible cultural materials, as well as for identity formation and the development of group solidarity. Future research should consider how variations in cultural distributors and in cultural interaction spaces affect audience reception, interpretation, and use of cultural objects.

scholarly journals An Examination of the Empirical Literature: Gifted Education in the Australian Context

2018 ◽  
Vol 42 (1) ◽  
pp. 64-84 ◽  
Author(s):  
Ivan Luburic ◽  
Jennifer L. Jolly
Keyword(s):  
Empirical Research ◽  
North American ◽  
Gifted Education ◽  
Empirical Literature ◽  
Future Research ◽  
Future Directions ◽  
Research And Practice ◽  
Current Trends ◽  
Australian Context ◽  
Research Themes

Gifted education as a field of research in Australia is relatively young when compared with its North American counterparts. A reflection of how the field of gifted education has developed from 1983 to 2017 in this context allows for observations of previous research and current trends, and how these may influence future directions for the field. Empirical research published in peer-reviewed journals is one metric that can be used to undertake this reflection, including the individuals responsible for the research, the setting where the research is undertaken, and outlets where resulting findings are published, as well as the research themes that dominate research agendas. Longitudinally, these metrics are part of the narrative that construct Australian gifted education. Reflecting on how the field developed provides an understanding of how research and practice have evolved and what future research and innovations are possible.

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