Harry Kipke punting as Fielding Yost watches fb8

[some dirt and damage on original cleaned up using photo editor]

Circannual rhythms of maturation in the female rainbow trout and their entrainment by changes in photoperiod

The importance of endogenous rhythms in the photoperiodic control of the annual reproduction cycle in female rainbow trout was investigated. The effect of photoperiod regimes on the different stages of maturation was assessed by recording the timing of ovulation and from quantifying associated changes in serum oestradiol-17,testosterone and total calcium. Maintained under constant 6L:18D and constant temperature for up to four years, rainbow trout exhibited an endogenous rhythm of maturation with a periodicity of approximately one year. This rhythm of maturation appears to be driven by an autonomous circannual oscillator or clock which can be dissociated from the neuroendocrine mechanisms controlling gonadal maturation. Under conditions of constant 18L:6D or LL the periodicity of the maturation rhythm was 5.5-6 months; it is suggested that this periodicity may be caused by a splitting or uncoupling of at least two circannual clocks involved in the control of maturation. Abrupt changes in the length of the photoperiod act as a zeitgeber to entrain the endogenous rhythm of maturation. Whether the timing of maturation is advanced or delayed depends primarily on the direction of the change in photoperiod and its timing in relation to the phase of the rhythm, with the magnitude of the alteration in photoperiod having only a supplementary effect. The effect of specific changes in photoperiod on the entrainment of the maturation cycle can be described in terms of a phase-response curve. Photic information is transduced, probably by the pineal gland, into a daily rhythm of melatonin; exposure of rainbow trout to skeleton and resonance photoperiod regimes indicated that daylength measurement is effected by endogenous circadian clock(s) rather than by hour-glass mechanisms. A gating mechanism is closely associated with the circannual clock which determines the timing of onset of maturation in virgin female rainbow trout, only allowing fish that have attained a threshold stage of development to undergo gonadal maturation. Collectively the results support the hypothesis that the female rainbow trout exhibits an endogenous circannual rhythm of maturation which can be entrained by changes in photoperiod.

A timescale for diatom evolution based on four molecular markers: reassessment of ghost lineages and major steps defining diatom evolution.

ABSTRACT. – Phylogenies and molecular clocks of the diatoms have largely been inferred from SSU rDNA sequences. A new phylogeny of diatoms was estimated using four gene markers SSU and LSU rDNA rbcL and psbA (total 4352 bp) with 42 diatom species. The four gene trees analysed with a maximum likelihood (ML) and Baysian (BI) analysis recovered a monophyletic origin of the new diatom classes with high bootstrap support, which has been controversial with single gene markers using single outgroups and alignments that do not take secondary structure of the SSU gene into account. The divergence time of the classes were calculated from a ML tree in the MultliDiv Time program using a Bayesian estimation allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. These divergence times are generally in agreement with those proposed by other clocks using single genes with the exception that the pennates appear much earlier and suggest a longer Cretaceous fossil record that has yet to be sampled. Ghost lineages (i.e. the discrepancy between first appearance (FA) and molecular clock age of origin from an extant taxon) were revealed in the pennate lineage, whereas those ghost lineages in the centric lineages previously reported by others are reviewed and referred to earlier literature.

A timescale for diatom evolution based on four molecular markers: reassessment of ghost lineages and major steps defining diatom evolution.

ABSTRACT. – Phylogenies and molecular clocks of the diatoms have largely been inferred from SSU rDNA sequences. A new phylogeny of diatoms was estimated using four gene markers SSU and LSU rDNA rbcL and psbA (total 4352 bp) with 42 diatom species. The four gene trees analysed with a maximum likelihood (ML) and Baysian (BI) analysis recovered a monophyletic origin of the new diatom classes with high bootstrap support, which has been controversial with single gene markers using single outgroups and alignments that do not take secondary structure of the SSU gene into account. The divergence time of the classes were calculated from a ML tree in the MultliDiv Time program using a Bayesian estimation allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. These divergence times are generally in agreement with those proposed by other clocks using single genes with the exception that the pennates appear much earlier and suggest a longer Cretaceous fossil record that has yet to be sampled. Ghost lineages (i.e. the discrepancy between first appearance (FA) and molecular clock age of origin from an extant taxon) were revealed in the pennate lineage, whereas those ghost lineages in the centric lineages previously reported by others are reviewed and referred to earlier literature.

Using passive acoustics and shore based surveys to investigate the use of Lundy Island’s near shore water by small odontocetes

The use of waters around Lundy by dolphins and porpoises was measured using summer shore-based watches and passive acoustic surveillance between July 2011 and July 2012. Common dolphins (Delphinus delphis) were the only cetacean species observed during shore-based surveys. C-PODs moored on the Ethel and MV Robert wrecks close to the Lundy coast showed a peak in delphinid vocal activity during August 2011. Passive acoustic detections of harbour porpoises (Phocoena phocoena) were highest during ebb tidal phases and most often associated with the tidal rip at the south of the island. These findings show tidal and monthly influences on odontocete behaviour and highlight the value of continuous, passive acoustic monitoring for these highly mobile marine predators around Lundy.

Degenerate mixtures of rubidium and ytterbium for engineering open quantum systems

In the last two decades, experimental progress in controlling cold atoms and ions now allows us to manipulate fragile quantum systems with an unprecedented degree of precision. This has been made possible by the ability to isolate small ensembles of atoms and ions from noisy environments, creating truly closed quantum systems which decouple from dissipative channels. However in recent years, several proposals have considered the possibility of harnessing dissipation in open systems, not only to cool degenerate gases to currently unattainable temperatures, but also to engineer a variety of interesting many-body states. This thesis will describe progress made towards building a degenerate gas apparatus that will soon be capable of realizing these proposals. An ultracold gas of ytterbium atoms, trapped by a species-selective lattice will be immersed into a Bose-Einstein condensate (BEC) of rubidium atoms which will act as a bath. Here we describe the challenges encountered in making a degenerate mixture of rubidium and ytterbium atoms and present two experiments performed on the path to creating a controllable open quantum system. The first experiment will describe the measurement of a tune-out wavelength where the light shift of $\Rb{87}$ vanishes. This wavelength was used to create a species-selective trap for ytterbium atoms. Furthermore, the measurement of this wavelength allowed us to extract the dipole matrix element of the $5s \rightarrow 6p$ transition in $\Rb{87}$ with an extraordinary degree of precision. Our method to extract matrix elements has found use in atomic clocks where precise knowledge of transition strengths is necessary to account for minute blackbody radiation shifts. The second experiment will present the first realization of a degenerate Bose-Fermi mixture of rubidium and ytterbium atoms. Using a three-color optical dipole trap (ODT), we were able to create a highly-tunable, species-selective potential for rubidium and ytterbium atoms which allowed us to use $\Rb{87}$ to sympathetically cool $\Yb{171}$ to degeneracy with minimal loss. This mixture is the first milestone creating the lattice-bath system and will soon be used to implement novel cooling schemes and explore the rich physics of dissipation.