Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Cannon, Barbara, and Jan Nedergaard. Brown Adipose Tissue: Function and Physiological Significance. Physiol Rev 84: 277–359, 2004; 10.1152/physrev.00015.2003.—The function of brown adipose tissue i...

Brown Adipose Tissue: Function and Physiological Significance

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

Polyploids — organisms that have multiple sets of chromosomes — are common in certain plant and animal taxa, and can be surprisingly stable. The evidence that has emerged from genome analyses also indicates that many other eukaryotic genomes have a polyploid ancestry, suggesting that both humans and most other eukaryotes have either benefited from or endured polyploidy. Studies of polyploids soon after their formation have revealed genetic and epigenetic interactions between redundant genes. These interactions can be related to the phenotypes and evolutionary fates of polyploids. Here, I consider the advantages and challenges of polyploidy, and its evolutionary potential.

/pdf/the-advantages-and-disadvantages-of-being-polyploid-3szbdyr9u1.pdf

The advantages and disadvantages of being polyploid

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Divergence between incipient species remains an incompletely understood process Hybrid zones provide great research potential, reflecting natural organismal genomic interactions and gene evolution in a variety of recombinants over generations While sex chromosomes are known evolutionary drivers of reproductive isolation, empirical population genetics has mostly examined species with heteromorphic sex chromosomes We recently reported restricted introgression at sex-linked markers in an amphibian system with homomorphic sex chromosomes (Hyla), consistent with a large X-effect, designating a greater role of sex chromosomes in driving hybrid incompatibilities Here, using a similar approach, we examined two hybrid zones of Palearctic green toads (Bufo viridis subgroup), involving several lineages that arose at different times and form secondary contacts We find no evidence for differential introgression of sex-linked versus autosomal markers across both zones This absence of large X-effects in Bufo indicates that, unlike in Hyla, hybrid incompatibilities may not result from the faster-heterogametic sex and faster-male aspects of Haldane's rule The recent suppression of XY recombination in Hyla but not in Bufo may have driven greater divergence between Hyla sex chromosomes, causing stronger reproductive isolation Alternatively, stronger linkage among Hyla's sex-linked markers could restrict introgression We hypothesize that the degree of sex-specific recombination may condition the importance of homomorphic sex chromosomes in speciation

/pdf/introgression-across-hybrid-zones-is-not-mediated-by-large-x-3n4px4jhrc.pdf

Introgression across Hybrid Zones Is Not Mediated by Large X-Effects in Green Toads with Undifferentiated Sex Chromosomes.

In contrast with mammals and birds, most poikilothermic vertebrates feature structurally undifferentiated sex chromosomes, which may result either from frequent turnovers, or from occasional events of XY recombination. The latter mechanism was recently suggested to be responsible for sex-chromosome homomorphy in European tree frogs (Hyla arborea). However, no single case of male recombination has been identified in large-scale laboratory crosses, and populations from NW Europe consistently display sex-specific allelic frequencies with male-diagnostic alleles, suggesting the absence of recombination in their recent history. To address this apparent paradox, we extended the phylogeographic scope of investigations, by analyzing the sequences of three sex-linked markers throughout the whole species distribution. Refugial populations (southern Balkans and Adriatic coast) show a mix of X and Y alleles in haplotypic networks, and no more within-individual pairwise nucleotide differences in males than in females, testifying to recurrent XY recombination. In contrast, populations of NW Europe, which originated from a recent postglacial expansion, show a clear pattern of XY differentiation; the X and Y gametologs of the sex-linked gene Med15 present different alleles, likely fixed by drift on the front wave of expansions, and kept differentiated since. Our results support the view that sex-chromosome homomorphy in H. arborea is maintained by occasional or historical events of recombination; whether the frequency of these events indeed differs between populations remains to be clarified.

/pdf/range-wide-sex-chromosome-sequence-similarity-supports-suy6whwivw.pdf

Range-wide sex-chromosome sequence similarity supports occasional XY recombination in European tree frogs (Hyla arborea).

Resting oxygen consumption was elevated by 30% in young rats fed a cafeteria diet compared with their chow-fed controls and by 22% in cafeteria-fed, adrenalectomized (ADX) rats compared with the ADX chow-fed group, but injection of propranolol reduced oxygen consumption in the cafeteria-fed animals and abolished these differences Brown adipose tissue (BAT) mass was increased by cafeteria feeding, and the activity of the mitochondrial proton conductance pathway (assessed from purine nucleotide binding) was enhanced by adrenalectomy and by cafeteria feeding Norepinephrine turnover in BAT (determined from the time-dependent loss of tissue [3H]norepinephrine specific activity) was increased by 105% in sham-operated, cafeteria-fed rats, by 142% in chow-fed ADX rats, and by 400% in cafeteria-fed ADX rats, compared with chow-fed controls Cardiac norepinephrine turnover was elevated by 80% in sham-operated, cafeteria-fed rats, but unaffected by adrenalectomy These data indicate that the enhanced thermogenesis and BAT activity induced by adrenalectomy in chow- or cafeteria-fed rats is due to increased sympathetic activity in the tissue

Thermogenesis and sympathetic activity in BAT of overfed rats after adrenalectomy.

Experiments were performed to investigate the effect of age and genotype on brown adipose tissue thermogenesis in Zucker rats. Specific [3H]GDP binding to interscapular brown adipose tissue mitochondria ( IBATM ) was reduced in 14-day-old preobese fa/fa rats and remained lower after weaning. A gene-dosage effect of the recessive fa gene was observed in 8- to 10-wk-old rats in both IBATM [3H]GDP binding and the thermic effect of a balanced meal (50 kJ Complan ), measured by indirect calorimetry. In each case the heterozygote (Fa/fa) group had a value intermediate between those of obese (fa/fa) and the homozygous lean (Fa/Fa) groups. Norepinephrine increased IBATM [3H]GDP binding to similar levels in lean (Fa/fa) and obese (fa/fa) rats and induced similar increases in oxygen consumption in Fa/Fa, Fa/fa, and fa/fa rats. It is concluded that the impaired, diet-related brown adipose tissue thermogenesis is closely related to the primary gene defect in the obese rat. This defect may result from misregulation of the autonomic nervous system.

Effect of age and gene dosage on brown adipose tissue of Zucker obese fa/fa rats

We show that MED15, a key component of the transcription complex Mediator, lies within the nonrecombining segment of nascent sex chromosomes in the male-heterogametic Hyla arborea. Both X and Y alleles are expressed during embryonic development and differ by three frame-preserving indels (eight amino acids in total) within their glutamine-rich central part. These changes have the potential to affect the conformation of the Mediator complex and to activate genes in a sex-specific way and might thus represent the first steps toward the acquisition of a male-specific function. Alternatively, they might result from an ancestral neutral polymorphism, with different alleles picked by chance on the X and Y chromosomes when MED15 was trapped in the nonrecombining segment.

https://serval.unil.ch/resource/serval:BIB_33B31B102586.P001/REF.pdf

Matthias Stöck

Papers

Introgression across Hybrid Zones Is Not Mediated by Large X-Effects in Green Toads with Undifferentiated Sex Chromosomes.

Range-wide sex-chromosome sequence similarity supports occasional XY recombination in European tree frogs (Hyla arborea).

Thermogenesis and sympathetic activity in BAT of overfed rats after adrenalectomy.

Effect of age and gene dosage on brown adipose tissue of Zucker obese fa/fa rats

A key transcription cofactor on the nascent sex chromosomes of European tree frogs (Hyla arborea).