scholarly journals Evolution of the canonical sex chromosomes of the guppy and its relatives

2021 ◽  
Author(s):  
Mark Kirkpatrick ◽  
Jason M Sardell ◽  
Brendan J Pinto ◽  
Groves Dixon ◽  
Catherine L Peichel ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Best Practices ◽  
Sex Chromosomes ◽  
Linkage Mapping ◽  
Poecilia Reticulata ◽  
Model Systems ◽  
History Of ◽  
Suppressed Recombination ◽  
Close Relatives

Abstract The sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as humans and Drosophila melanogaster, and they carry many of the genes responsible for the males’ dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here we address these controversies by reviewing the evidence and reanalyzing data. We find no evidence of a nonrecombining sex determining region (SDR) or evolutionary strata in P. reticulata. Further, we find that the data most strongly support the hypothesis that the SDRs of two close relatives of the guppy, P. wingei and Micropoecilia picta, evolved independently after their lineages diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.

scholarly journals Evolution of the canonical sex chromosomes of the guppy and its relatives

2020 ◽  
Author(s):  
M. Kirkpatrick ◽  
G. Dixon ◽  
J.M. Sardell ◽  
M. Schartl ◽  
C. L. Peichel
Keyword(s):  
Drosophila Melanogaster ◽  
Best Practices ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Linkage Mapping ◽  
Poecilia Reticulata ◽  
Model Systems ◽  
History Of ◽  
Suppressed Recombination ◽  
Close Relatives

AbstractThe sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as mammals and Drosophila melanogaster, and they carry many of the genes responsible for the males’ dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here we address these controversies by reviewing the evidence and reanalyzing data. We find no support for a nonrecombining sex determining region (SDR) or evolutionary strata in P. reticulata. We confirm that its congener P. picta has evolved dosage compensation across all of its X chromosome. Last, we do not find evidence that the nonrecombining SDRs of P. picta and P. wingei descend from a common ancestral SDR, and suggest instead that suppressed recombination between the X and Y evolved independently after the two species diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.

scholarly journals Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

2019 ◽  
Vol 116 (38) ◽  
pp. 19031-19036 ◽  
Author(s):  
Iulia Darolti ◽  
Alison E. Wright ◽  
Benjamin A. Sandkam ◽  
Jake Morris ◽  
Natasha I. Bloch ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Poecilia Reticulata ◽  
Sex Chromosome ◽  
Sequencing Data ◽  
Chromosome Differentiation ◽  
Y Chromosomes ◽  
Shared Ancestry ◽  
Suppressed Recombination

Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

scholarly journals Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

2019 ◽  
Author(s):  
Iulia Darolti ◽  
Alison E. Wright ◽  
Benjamin A. Sandkam ◽  
Jake Morris ◽  
Natasha I. Bloch ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Poecilia Reticulata ◽  
Sex Chromosome ◽  
Sequencing Data ◽  
Chromosome Differentiation ◽  
Shared Ancestry ◽  
Sex Chromosome System ◽  
Suppressed Recombination

ABSTRACTOnce recombination is halted between the X and Y chromosome, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about variation in sex chromosome differentiation within clades. Here, we combined whole genome and transcriptome sequencing data to characterise the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged 30 mya. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata are largely homomorphic, with recombination persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely non-recombining and strikingly heteromorphic. ln addition to being highly divergent, the sex chromosome system in P. picta includes a neo-sex chromosome, the result of a fusion between the ancestral sex chromosome and part of chromosome 7. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of complete dosage compensation in this species, the first such documented case in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

scholarly journals Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms

2019 ◽  
Vol 116 (14) ◽  
pp. 6924-6931 ◽  
Author(s):  
Roberta Bergero ◽  
Jim Gardner ◽  
Beth Bader ◽  
Lengxob Yong ◽  
Deborah Charlesworth
Keyword(s):  
Sex Chromosomes ◽  
Poecilia Reticulata ◽  
Low Frequency ◽  
Male Meiosis ◽  
Chromosome 12 ◽  
Sexually Dimorphic ◽  
Recombination Suppression ◽  
Physical Maps ◽  
Suppressed Recombination ◽  
Male Coloration

It is often stated that polymorphisms for mutations affecting fitness of males and females in opposite directions [sexually antagonistic (SA) polymorphisms] are the main selective force for the evolution of recombination suppression between sex chromosomes. However, empirical evidence to discriminate between different hypotheses is difficult to obtain. We report genetic mapping results in laboratory-raised families of the guppy (Poecilia reticulata), a sexually dimorphic fish with SA polymorphisms for male coloration genes, mostly on the sex chromosomes. Comparison of the genetic and physical maps shows that crossovers are distributed very differently in the two sexes (heterochiasmy); in male meiosis, they are restricted to the termini of all four chromosomes studied, including chromosome 12, which carries the sex-determining locus. Genome resequencing of male and female guppies from a population also indicates sex linkage of variants across almost the entire chromosome 12. More than 90% of the chromosome carrying the male-determining locus is therefore transmitted largely through the male lineage. A lack of heterochiasmy in a related fish species suggests that it originated recently in the lineage leading to the guppy. Our findings do not support the hypothesis that suppressed recombination evolved in response to the presence of SA polymorphisms. Instead, a low frequency of recombination on a chromosome that carries a male-determining locus and has not undergone genetic degeneration has probably facilitated the establishment of male-beneficial coloration polymorphisms.

scholarly journals Ecology, Structure, and Evolution of Shigella Phages

2020 ◽  
Vol 7 (1) ◽  
pp. 121-141
Author(s):  
Sundharraman Subramanian ◽  
Kristin N. Parent ◽  
Sarah M. Doore
Keyword(s):  
Defense Mechanisms ◽  
Structural Information ◽  
Bacterial Species ◽  
Model Systems ◽  
Isolation And Characterization ◽  
Shigella Species ◽  
Recent Developments ◽  
History Of ◽  
Close Relatives ◽  
Host Evolution

Numerous bacteriophages—viruses of bacteria, also known as phages—have been described for hundreds of bacterial species. The Gram-negative Shigella species are close relatives of Escherichia coli, yet relatively few previously described phages appear to exclusively infect this genus. Recent efforts to isolate Shigella phages have indicated these viruses are surprisingly abundant in the environment and have distinct genomic and structural properties. In addition, at least one model system used for experimental evolution studies has revealed a unique mechanism for developing faster infection cycles. Differences between these bacteriophages and other well-described model systems may mirror differences between their hosts’ ecology and defense mechanisms. In this review, we discuss the history of Shigella phages and recent developments in their isolation and characterization and the structural information available for three model systems, Sf6, Sf14, and HRP29; we also provide an overview of potential selective pressures guiding both Shigella phage and host evolution.

Trying to Professionalize Expert Knowledge (Part I): The Short Life of the Municipal Administration Service, 1926-1933

Public Voices ◽  
2017 ◽  
Vol 15 (1) ◽  
pp. 9 ◽  
Author(s):  
Mordecai Lee
Keyword(s):  
Best Practices ◽  
Public Administration ◽  
Expert Knowledge ◽  
Building Blocks ◽  
Early History ◽  
Short Life ◽  
Organizational History ◽  
Municipal Administration ◽  
History Of ◽  
Wide Dissemination

One of the building blocks of the professionalization of American public administration was the recognition of the need for expert knowledge and the wide dissemination of that information to practitioners. Municipal civil servants could adopt and adapt these best practices in their localities. Such was the purpose of the Municipal Administration Service (1926-1933), initially founded by the National Municipal League and funded by the Rockefeller philanthropies. This article is an organizational history of the Service. It presents the life cycle of the agency, including its operations, funding, problems, and the behind-the-scenes public administration politics which led to its demise. In all, the Municipal Administration Service captures the early history of American public administration, its attempt to demonstrate that it was a full-fledged profession with recognized experts and managerial advice that ultimately proved unable to perpetuate itself.

Searching for Justice After the Holocaust

2019 ◽  
Author(s):  
Michael J. Bazyler ◽  
Kathryn Lee Boyd ◽  
Kristen L. Nelson ◽  
Rajika L. Shah
Keyword(s):  
Best Practices ◽  
Legal History ◽  
Holocaust Survivors ◽  
European Parliament ◽  
Slave Labor ◽  
Insurance Policies ◽  
The Holocaust ◽  
History Of ◽  
Nazi Era ◽  
Property Restitution

The Nazis and their cohorts stole mercilessly from the Jews of Europe. In the aftermath of the Holocaust, returning survivors had to navigate unclear and hostile legal paths to recover their stolen property from governments and neighbors who often had been complicit in their persecution and theft. While the return of Nazi-looted art and recent legal settlements involving dormant Swiss bank accounts, unpaid insurance policies and use of slave labor by German companies have been well-publicized, efforts by Holocaust survivors and heirs over the last 70 years to recover stolen land and buildings were forgotten. In 2009, 47 countries convened in Prague to deal with the lingering problem of restitution of prewar private, communal, and heirless property stolen during the Holocaust. The outcome was the Terezin Declaration on Holocaust Era Assets and Related Issues, aiming to “rectify the consequences” of the wrongful Nazi-era immovable property seizures. This book sets forth the legal history of Holocaust immovable property restitution in each of the Terezin Declaration signatory states. It also analyzes how each of the 47 countries has fulfilled the standards of the Guidelines and Best Practices of the Terezin Declaration. These standards were issued in 2010 in conjunction with the establishment of the European Shoah Legacy Institute (ESLI), a state-sponsored NGO created to monitor compliance. The book is based on the Holocaust (Shoah) Immovable Property Restitution Study commissioned by ESLI, written by the authors and issued in Brussels in 2017 before the European Parliament.

Network Visualization

2020 ◽  
pp. 351-367
Author(s):  
James Moody ◽  
Ryan Light
Keyword(s):  
Best Practices ◽  
Social Relationships ◽  
Visual Display ◽  
Network Visualization ◽  
Making Sense ◽  
Complex Information ◽  
Underlying Network ◽  
History Of ◽  
Effective Network ◽  
Data Visualizations

This chapter provides an overview of social network visualization. Network analysis encourages the visual display of complex information, but effective network diagrams, like other data visualizations, result from several best practices. After a brief history of network visualization, the chapter outlines several of those practices. It highlights the role that network visualizations play as heuristics for making sense of networked data and translating complicated social relationships, such as those that are dynamic, into more comprehensible structures. The goal in this chapter is to help identify the methods underlying network visualization with an eye toward helping users produce more effective figures.

scholarly journals Multi-Locus Selection and the Structure of Variation at the white Gene of Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 635-645 ◽  
Author(s):  
David A Kirby ◽  
Wolfgang Stephan
Keyword(s):  
Drosophila Melanogaster ◽  
White Gene ◽  
Transcriptional Unit ◽  
North American Population ◽  
Evolutionary Mechanisms ◽  
Locus Selection ◽  
Neutral Equilibrium ◽  
History Of ◽  
High Degree ◽  
Very High

Abstract We surveyed sequence variation and divergence for the entire 5972-bp transcriptional unit of the white gene in 15 lines of Drosophila melanogaster and one line of D. simulans. We found a very high degree of haplotypic structuring for the polymorphisms in the 3′ half of the gene, as opposed to the polymorphisms in the 5′ half. To determine the evolutionary mechanisms responsible for this pattern, we sequenced a 1612-bp segment of the white gene from an additional 33 lines of D. melanogaster from a European and a North American population. This 1612-bp segment encompasses an 834bp region of the white gene in which the polymorphisms form high frequency haplotypes that cannot be explained by a neutral equilibrium model of molecular evolution. The small number of recombinants in the 834bp region suggests epistatic selection as the cause of the haplotypic structuring, while an investigation of nucleotide diversity supports a directional selection hypothesis. A multi-locus selection model that combines features from both-hypotheses and takes the recent history of D. melanogaster into account may be the best explanation for these data.

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