State Standing and National Injunctions

Most of the growing literature on national injunctions makes only passing mention, if at all, of states being plaintiffs or of the appropriateness of state standing and how it might bear on the geographic scope of an injunction. This Essay undertakes to fill that gap in a more extended way. Part I of the Essay addresses the issue of state standing in suits against the federal government, and argues that such standing is well grounded in the traditional parens patriae powers of states and should be permitted to protect the health, welfare, and natural resources of their citizens. That is, courts should permit states to have standing under somewhat relaxed criteria as compared to what private plaintiffs must show. Part II turns to national injunctions; discusses the recent increases in the issuance of those decrees; and explores the controversy over when, if ever, federal courts possess powers under equity or standing criteria to bind the entire nation. Part III addresses both topics in a coordinated manner. It acknowledges the benefit of states suing to protect federalism interests against the incursions of the federal government, but also addresses the pathologies of one or more states bringing suit, particularly in the partisanship demonstrated by states led by attorneys general or governors of states from the same political party suing to stop the actions of a presidential administration of a different party. While states in some circumstances have standing to sue, it does not automatically follow that even when successful the entire nation should be subject to an injunction. Rather, we propose an alternative to the dichotomy that courts always (or almost always) or, conversely, never have authority to issue such injunctions. We support the possibility of nationwide injunctions, but before issuing such decrees, courts should take into account factors such as the number and geographic and partisan diversity of the states, who (attorney general or governor) is representing a state, and which one or more states are opposing the decrees, as parties or amici curiae. These criteria would better inform and integrate judicial consideration of state standing and national injunctions when they arise in the same case. Finally, Part III critically examines various possible statutory solutions to the problems of national injunctions, including vesting exclusive jurisdiction of suits seeking that relief in the District of Columbia, or requiring that they be heard by a three-judge district court

Individual organisms as units of analysis: Bayesian-clustering alternatives in population genetics.

Population genetic analyses traditionally focus on the frequencies of alleles or genotypes in 'populations' that are delimited a priori. However, there are potential drawbacks of amalgamating genetic data into such composite attributes of assemblages of specimens: genetic information on individual specimens is lost or submerged as an inherent part of the analysis. A potential also exists for circular reasoning when a population's initial identification and subsequent genetic characterization are coupled. In principle, these problems are circumvented by some newer methods of population identification and individual assignment based on statistical clustering of specimen genotypes. Here we evaluate a recent method in this genre--Bayesian clustering--using four genotypic data sets involving different types of molecular markers in non-model organisms from nature. As expected, measures of population genetic structure (F(ST) and phiST) tended to be significantly greater in Bayesian a posteriori data treatments than in analyses where populations were delimited a priori. In the four biological contexts examined, which involved both geographic population structures and hybrid zones, Bayesian clustering was able to recover differentiated populations, and Bayesian assignments were able to identify likely population sources of specific individuals

Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes.

The genomes of ray-finned fishes (Actinopterygii) are well known for their evolutionary dynamism as reflected by drastic alterations in DNA content often via regional and whole-genome duplications, differential patterns of gene silencing or loss, shifts in the insertion-to-deletion ratios of genomic segments, and major re-patternings of chromosomes via non-homologous recombination. In sharp contrast, chromosome numbers in somatic karyotypes have been highly conserved over vast evolutionary timescales - a histogram of available counts is strongly leptokurtic with more than 50% of surveyed species displaying either 48 or 50 chromosomes. Here we employ comparative phylogenetic analyses to examine the evolutionary history of alterations in fish chromosome numbers. The most parsimonious ancestral state for major actinopterygiian clades is 48 chromosomes. When interpreted in a phylogenetic context, chromosome numbers evidence many recent instances of polyploidization in various lineages but there is no clear indication of a singular polyploidization event that has been hypothesized to have immediately preceded the teleost radiation. After factoring out evident polyploidizations, a correlation between chromosome numbers and genome sizes across the Actinopterygii is marginally statistically significant (p = 0.012) but exceedingly weak (R (2) = 0.0096). Overall, our phylogenetic analysis indicates a mosaic evolutionary pattern in which the forces that govern labile features of fish genomes must operate largely independently of those that operate to conserve chromosome numbers

The unique genomic properties of sex-biased genes: Insights from avian microarray data

In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue

Sexual selection and the evolution of condition-dependence: an experimental test at two resource levels

Stronger condition-dependence in sexually selected traits is well-documented, but how this relationship is established remains unknown. Moreover, resource availability can shape responses to sexual selection, but resource effects on the relationship between sexual selection and condition-dependence are also unknown. In this study, we directly test the hypotheses that sexual selection drives the evolution of stronger-condition-dependence and that resource availability affects the outcome, by evolving fruit flies (Drosophila melanogaster) under relatively strong or weak sexual selection (through varied sex ratios) and at resource-poor or resource-rich adult diets. We then experimentally manipulated condition via developmental diet and assessed condition-dependence in adult morphology, behavior, and reproduction. We observed stronger condition-dependence in female size in male-biased populations and in female ovariole production in resource-limited populations. However, we found no evidence that male condition-dependence increased in response to sexual selection, or that responses depended on resource levels. These results offer no support for the hypotheses that sexual selection increases male condition-dependence or that sexual selection's influence on condition-dependence is influenced by resource availability. Our study is, to our knowledge, the first experimental test of these hypotheses. If the results we report are general, then sexual selection's influence on the evolution of condition-dependence may be less important than predicted

The Ontogeny and Evolution of Sex-Biased Gene Expression in Drosophila melanogaster

Sexually dimorphic phenotypes are thought to largely result from sex differences in gene expression, and genes with sex-biased expression have been well characterized in adults of many species. Although most sexual dimorphisms manifest in adults, many result from sex-specific developmental trajectories, implying that juveniles may exhibit significant levels of sex-biased expression. However, it is unclear how much sex-biased expression occurs before reproductive maturity and whether preadult sex-biased genes should exhibit the same evolutionary dynamics observed for adult sex-biased genes. In order to understand the continuity, or lack thereof, and evolutionary dynamics of sex-biased expression throughout the life cycle, we examined sex-biased genes in pre-gonad tissue of two preadult stages and compared them with the adult gonad of Drosophila melanogaster. We found that the majority of the genome is sex-biased at some point in the life cycle, with some genes exhibiting conserved sex-biased expression and others displaying stage-specific sex bias. Our results also reveal a far more complex pattern of evolution for sex-biased genes throughout development. The most rapid evolutionary divergence occurred in genes expressed only in larvae within each sex, compared with continuously expressed genes. In females—but not males—this pattern appeared to be due to relaxed purifying selection in larva-limited genes. Furthermore, genes that retained male bias throughout life evolved more rapidly than stage-specific male-biased genes, due to stronger purifying selection in stage-specific genes. However, female-biased genes that were specific to larvae evolved most rapidly, a pattern that could not be definitively attributed to differences in adaptive evolution or purifying selection, suggesting that pleiotropic constraints on protein-coding sequences can arise when genes are broadly expressed across developmental stages. These results indicate that the signature of sex-specific selection can be detected well before reproductive maturity and is strongest during development

The long and winding road leading to the successful introgression of downy mildew resistance into onion

Downy mildew resistance originating from Allium roylei Stearn provides a complete resistance to onions and is based on one, dominant gene. Since A. roylei can successfully be hybridized with onion (A. cepa L.), a breeding scheme aimed at the introgression of this gene was initiated ca. 20 years ago. Several setbacks in this programme were encountered, firstly the identified molecular marker linked to the downy mildew resistance locus became increasingly difficult to use and finally lost its discriminating power and secondly the final step, making homozygous introgression lines (ILs), turned out to be more difficult then was hoped. GISH analysis showed that the chromosomal region harbouring the resistance locus was the only remaining piece of A. roylei in the nuclear background of onion and it also confirmed that this region was located on the distal end of chromosome 3. It was hypothesized that some factor present in the remaining A. roylei region was lethal when homozygously present in an onion genetic background. The identification of an individual with a smaller and more distally located introgression fragment and homozygous ILs in its progeny validated this hypothesis. With the help of these nearly isogenic lines four AFLP® markers closely linked to the resistance gene were identified, which can be used for marker-aided selection. The introduction of downy mildew resistance caused by Peronospora destructor into onion is a significant step forward in the development of environmentally-friendly onion cultivars.<br/>Downy mildew resistance originating from Allium roylei Stearn provides a complete resistance to onions and is based on one, dominant gene. Since A. roylei can successfully be hybridized with onion (A. cepa L.), a breeding scheme aimed at the introgression of this gene was initiated ca. 20 years ago. Several setbacks in this programme were encountered, firstly the identified molecular marker linked to the downy mildew resistance locus became increasingly difficult to use and finally lost its discriminating power and secondly the final step, making homozygous introgression lines (ILs), turned out to be more difficult then was hoped. GISH analysis showed that the chromosomal region harbouring the resistance locus was the only remaining piece of A. roylei in the nuclear background of onion and it also confirmed that this region was located on the distal end of chromosome 3. It was hypothesized that some factor present in the remaining A. roylei region was lethal when homozygously present in an onion genetic background. The identification of an individual with a smaller and more distally located introgression fragment and homozygous ILs in its progeny validated this hypothesis. With the help of these nearly isogenic lines four AFLP (R) markers closely linked to the resistance gene were identified, which can be used for marker-aided selection. The introduction of downy mildew resistance caused by Peronospora destructor into onion is a significant step forward in the development of environmentally-friendly onion cultivars

Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation.

Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution