History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137755/1/evo13278-sup-0001-SuppMat.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137755/2/evo13278.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/137755/3/evo13278_am.pd

Time and time again: unisexual salamanders (genus Ambystoma) are the oldest unisexual vertebrates

<p>Abstract</p> <p>Background</p> <p>The age of unisexual salamanders of the genus <it>Ambystoma </it>is contentious. Recent and ancient evolutionary histories of unisexual <it>Ambystoma </it>were proposed by a few separate studies that constructed phylogenies using mitochondrial DNA markers (cytochrome b gene vs. non-coding region). In contrast to other studies showing that unisexual <it>Ambystoma </it>represent the most ancient unisexual vertebrates, a recent study by Robertson et al. suggests that this lineage has a very recent origin of less than 25,000 years ago.</p> <p>Results</p> <p>We re-examined the phylogenetic relationship of the unisexuals to <it>A. barbouri </it>from various populations using both mitochondrial markers as well as the complete mitochondrial genomes of <it>A. barbouri </it>and a unisexual individual from Kentucky. Lineage dating was conducted using BEAST and MultiDivTime on a complete mitochondrial genome phylogeny. Our results support a monophyletic lineage for unisexual <it>Ambystoma </it>that shares its most recent common ancestor with an <it>A. barbouri </it>lineage from western Kentucky. In contrast to the Robertson et al.'s study, no <it>A. barbouri </it>individual shared an identical or almost identical cytochrome b haplotype with any unisexual. Molecular dating supports an early Pliocene origin for the unisexual linage (~5 million years ago). We propose that a unisexual-like cytochrome b <it>numt </it>(or pseudogene) exists in the controversial <it>A. barbouri </it>individuals from Kentucky, which was likely the cause of an erroneous phylogeny and time estimate in Robertson et al.'s study.</p> <p>Conclusion</p> <p>We reject a recent origin of unisexual <it>Ambystoma </it>and provide strong evidence that unisexual <it>Ambystoma </it>are the most ancient unisexual vertebrates known to exist. The likely presence of an ancient cytochrome b <it>numt </it>in some Kentucky <it>A. barbouri </it>represents a molecular "fossil" reinforcing the hypothesis that these individuals are some of the closest extant relatives to unisexual <it>Ambystoma</it>.</p

The prevalence of genome replacement in unisexual salamanders of the genus Ambystoma (Amphibia, Caudata) revealed by nuclear gene genealogy

<p>Abstract</p> <p>Background</p> <p>Unisexual salamanders of the genus <it>Ambystoma </it>exemplify the most ancient lineage of unisexual vertebrates and demonstrate an extremely flexible reproductive system. Unisexual <it>Ambystoma </it>interact with and incorporate genomes from two to four sexual species (<it>A. laterale</it>, <it>A. jeffersonianum</it>,<it>A. texanum</it>, and <it>A. tigrinum</it>), to generate more than 20 genome compositions or biotypes. Unisexual ploidy levels range from diploid to pentaploid, but all contain at least one <it>A. laterale </it>(L) genome. Replacement of nuclear genomes might be responsible for the evolutionary longevity of unisexual <it>Ambystoma </it>but direct evidence for the prevalence of genome replacement in natural populations is absent. Two major puzzling questions have remained unanswered over the last few decades: 1) is genome replacement a common reproductive method in various unisexual populations and, 2) is there an ancient "L" genome that persists in various unisexual genome compositions.</p> <p>Results</p> <p>We examined 194 unisexual and 89 <it>A. laterale </it>specimens from 97 localities throughout their range and constructed a genealogy of the "L" genomes using a nuclear DNA marker (L-G1C12) to answer the above questions. Six L-G1C12 haplotypes (A-F) were shared by individuals in various <it>A. laterale </it>and unisexual populations. The general geographical distribution of the haplotypes in unisexual populations conformed to those found in <it>A. laterale</it>, indicating that "L" genomes in unisexuals are obtained from sympatric or nearby populations of <it>A. laterale</it>.</p> <p>Conclusion</p> <p>Our data demonstrate that genome replacement frequently occurs in unisexual <it>Ambystoma </it>across their range, and support previous speculations that genome replacement is an important reproductive mechanism that can enhance their evolutionary longevity. Our results show that there is no ancient "L" genome in the unisexual lineages, and no particular "L" genome is favored in any unisexual individual. The presence of an "L" genome in all unisexuals implies that it is important to the maintenance of unisexuals. Nuclear gene genealogy is a powerful tool to examine the historical interaction between sperm-dependent unisexuals and their sexual sperm donors. This methodology could be applicable to many other unisexual lineages to improve our understanding of their reproduction and their ability to persist.</p

Primordial Black Hole Mass Function with Mass Gap

Primordial black holes (PBHs) are mainly characterized by their mass function, in which there may be some huge suppression for certain mass spans. If this is the case, the absence of these PBHs will form mass gaps. In this paper, we investigate the PBH mass function with mass gap. Firstly, to obtain a data-supported PBH mass function with mass gap for subsolar masses PBHs, we fine-tune the coefficients of a model-independent power spectrum of primordial curvature perturbations. Then we take this unique PBH mass function into consideration and calculate the energy density spectrum of the stochastic gravitational wave background from PBH mergers. We find the location of its first peak almost has no relationship with the mass gap and is only determined by the probability distribution of frequencies at which PBH binaries merge. Apart from the first peak, there must be an accompanying smaller trough at higher frequency resulting from the mass gap. Therefore, the detection of this smaller trough will provide more information about inflation and PBH formation.Comment: 8 pages, 5 figure

Olmesartan restores the protective effect of remote ischemic perconditioning against myocardial ischemia/reperfusion injury in spontaneously hypertensive rats

OBJECTIVES: Remote ischemic perconditioning is the newest technique used to lessen ischemia/reperfusion injury. However, its effect in hypertensive animals has not been investigated. This study aimed to examine the effect of remote ischemic perconditioning in spontaneously hypertensive rats and determine whether chronic treatment with Olmesartan could influence the effect of remote ischemic perconditioning. METHODS: Sixty rats were randomly divided into six groups: vehicle-sham, vehicle-ischemia/reperfusion injury, vehicle-remote ischemic perconditioning, olmesartan-sham, olmesartan-ischemia/reperfusion and olmesartan-remote ischemic perconditioning. The left ventricular mass index, creatine kinase concentration, infarct size, arrhythmia scores, HIF-1α mRNA expression, miR-21 expression and miR-210 expression were measured. RESULTS: Olmesartan significantly reduced the left ventricular mass index, decreased the creatine kinase concentration, limited the infarct size and reduced the arrhythmia score. The infarct size, creatine kinase concentration and arrhythmia score during reperfusion were similar for the vehicle-ischemia/reperfusion group and vehicle-remote ischemic perconditioning group. However, these values were significantly decreased in the olmesartan-remote ischemic perconditioning group compared to the olmesartan-ischemia/reperfusion injury group. HIF-1α, miR-21 and miR-210 expression were markedly down-regulated in the Olmesartan-sham group compared to the vehicle-sham group and significantly up-regulated in the olmesartan-remote ischemic perconditioning group compared to the olmesartan-ischemia/reperfusion injury group. CONCLUSION: The results indicate that (1) the protective effect of remote ischemic perconditioning is lost in vehicle-treated rats and that chronic treatment with Olmesartan restores the protective effect of remote ischemic perconditioning; (2) chronic treatment with Olmesartan down-regulates HIF-1α, miR-21 and miR-210 expression and reduces hypertrophy, thereby limiting ischemia/reperfusion injury; and (3) recovery of the protective effect of remote ischemic perconditioning is related to the up-regulation of HIF-1α, miR-21 and miR-210 expression

Manganese coordination chemistry of bis(imino)phenoxide derived [2 + 2] Schiff-base macrocyclic ligands

The [2 + 2] Schiff base macrocycles [2,2'-(CH₂CH₂)(C₆H₄N)₂-2,6-(4-RC₆H₃OH)]₂ (IʳH₂), upon reaction with MnCl₂ (two equivalents) afforded the bimetallic complex [Cl₃Mn(NCMe)][MnCl(IᵗᵇᵘH₂)] (2). Under similar conditions, use of the related [2 + 2] oxy-bridged macrocycle [2,2'-O(C₆H₄N=CH)₂4-RC₆H₃OH] (IIʳH₂), afforded the bimetallic complexes [(MnCl)₂IIʳ] (R = Me 3, tBu 4), whilst the macrocycle derived from 1,2-diaminobenzene and 5,5'-di-tert-butyl-2,2'-dihydroxy-3,3'-methylenedibenzaldehyde (IIIH₄) afforded the complex [(MnCl)₂(III)]·2MeCN (5·2MeCN). For comparative studies, the salt complexes [2,6-(ArNHCH)₂-4-MeC₆H₂O][MnCl₃(NCMe)] (Ar = 2,4-Me₂C₆H₃, 6) and {[2,6-(ArNHCH)₂-4-MeC₆H₂O][MnCl}₂[MnCl₄]·8CH₂Cl₂ (Ar = 4-MeC₆H₄, 7·8CH₂Cl₂) were prepared. The crystal structures of 1 - 7 are reported (synchrotron radiation was necessary for complexes 1, 3 and 5). Complexes 1 - 7 (not 5) were screened for their potential to act as pre-catalysts for the ring opening polymerization (ROP) of ε-caprolactone; 3, 4 and 6, 7 were inactive, whilst 1 and 2 exhibited only poor activity low conversion (&lt;15 %) at temperatures above 60 °C

Fractonic Higher-Order Topological Phases in Open Quantum Systems

In this work, we study the generalization of decohered average symmetry-protected topological phases to open quantum systems with a combination of subsystem symmetries and global symmetries. In particular, we provide examples of two types of intrinsic average higher-order topological phases with average subsystem symmetries. A classification scheme for these phases based on generalized anomaly cancellation criteria of average symmetry is also discussed.Comment: 17 pages, 5 figure

High frequency impedance based fault location in distribution system with DGs

Distributed Generations (DGs) with power electronic devices and their control loops will cause distortion to the fault currents and result in errors for power frequency measurement based fault locations. This might jeopardize the distribution system fault restoration and reduce the grid resilience. The proposed method uses high frequency (up to 3kHz) fault information and short window measurement to avoid the influence of DG control loops. Applying the DG high frequency impedance model, faults can be accurately located by measuring the system high frequency line reactance. Assisted with the DG side recorded unsynchronized data, this method can be employed to distribution systems with multiple branches and laterals