Departures from neutrality induced by niche and relative fitness differences

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Theoretical Ecology 8 (2015): 449-465, doi:10.1007/s12080-015-0261-0.Breaking the core assumption of ecological equivalence in Hubbell’s “neutral theory of biodiversity” requires a theory of species differences. In one framework for characterizing differences between competing species, non-neutral interactions are said to involve both niche differences, which promote stable coexistence, and relative fitness differences, which promote competitive exclusion. We include both in a stochastic community model in order to determine if relative fitness differences compensate for changes in community structure and dynamics induced by niche differences, possibly explaining neutral theory’s apparent success. We show that species abundance distributions are sensitive to both niche and relative fitness differences, but that certain combinations of differences result in abundance distributions that are indistinguishable from the neutral case. In contrast, the distribution of species’ lifetimes, or the time between speciation and extinction, differs under all combinations of niche and relative fitness differences. The results from our model experiment are inconsistent with the hypothesis of “emergent neutrality” and support instead a hypothesis that relative fitness differences counteract effects of niche differences on distributions of abundance. However, an even more developed theory of interspecific variation appears necessary to explain the diversity and structure of non-neutral communities.The research was funded by NSF grant ECCS-0835847 and a postdoctoral scholarship from the Woods Hole Oceanographic Institution

Niche and fitness differences relate the maintenance of diversity to ecosystem function: reply

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134128/1/ecy20129361487.pd

Niche and fitness differences relate the maintenance of diversity to ecosystem function

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/116920/1/ecy20119251157.pd

Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae

The coexistence of competing species depends on the balance between their fitness differences, which determine their competitive inequalities, and their niche differences, which stabilise their competitive interactions. Darwin proposed that evolution causes species' niches to diverge, but the influence of evolution on relative fitness differences, and the importance of both niche and fitness differences in determining coexistence have not yet been studied together. We tested whether the phylogenetic distances between species of green freshwater algae determined their abilities to coexist in a microcosm experiment. We found that niche differences were more important in explaining coexistence than relative fitness differences, and that phylogenetic distance had no effect on either coexistence or on the sizes of niche and fitness differences. These results were corroborated by an analysis of the frequency of the co‐occurrence of 325 pairwise combinations of algal taxa in > 1100 lakes across North America. Phylogenetic distance may not explain the coexistence of freshwater green algae.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/100307/1/ele12182.pd

Benchmarking Quantum Processor Performance at Scale

As quantum processors grow, new performance benchmarks are required to capture the full quality of the devices at scale. While quantum volume is an excellent benchmark, it focuses on the highest quality subset of the device and so is unable to indicate the average performance over a large number of connected qubits. Furthermore, it is a discrete pass/fail and so is not reflective of continuous improvements in hardware nor does it provide quantitative direction to large-scale algorithms. For example, there may be value in error mitigated Hamiltonian simulation at scale with devices unable to pass strict quantum volume tests. Here we discuss a scalable benchmark which measures the fidelity of a connecting set of two-qubit gates over $N$ qubits by measuring gate errors using simultaneous direct randomized benchmarking in disjoint layers. Our layer fidelity can be easily related to algorithmic run time, via $\gamma$ defined in Ref.\cite{berg2022probabilistic} that can be used to estimate the number of circuits required for error mitigation. The protocol is efficient and obtains all the pair rates in the layered structure. Compared to regular (isolated) RB this approach is sensitive to crosstalk. As an example we measure a $N=80~(100)$ qubit layer fidelity on a 127 qubit fixed-coupling "Eagle" processor (ibm\_sherbrooke) of 0.26(0.19) and on the 133 qubit tunable-coupling "Heron" processor (ibm\_montecarlo) of 0.61(0.26). This can easily be expressed as a layer size independent quantity, error per layered gate (EPLG), which is here $1.7\times10^{-2}(1.7\times10^{-2})$ for ibm\_sherbrooke and $6.2\times10^{-3}(1.2\times10^{-2})$ for ibm\_montecarlo.Comment: 15 pages, 8 figures (including appendices

Decade-Spanning High-Precision Terahertz Frequency Comb

The generation and detection of a decade-spanning terahertz (THz) frequency comb is reported using two Ti:sapphire femtosecond laser oscillators and asynchronous optical sampling THz time-domain spectroscopy. The comb extends from 0.15 to 2.4 THz, with a tooth spacing of 80 MHz, a linewidth of 3.7 kHz, and a fractional precision of 1.8×10^(−9). With time-domain detection of the comb, we measure three transitions of water vapor at 10 mTorr between 1–2 THz with an average Doppler-limited fractional accuracy of 6.1×10^(−8). Significant improvements in bandwidth, resolution, and sensitivity are possible with existing technologies

A decade-spanning high-resolution asynchronous optical sampling terahertz time-domain and frequency comb spectrometer

We present the design and capabilities of a high-resolution, decade-spanning ASynchronous OPtical Sampling (ASOPS)-based TeraHertz Time-Domain Spectroscopy (THz-TDS) instrument. Our system employs dual mode-locked femtosecond Ti:Sapphire oscillators with repetition rates offset locked at 100 Hz via a Phase-Locked Loop (PLL) operating at the 60th harmonic of the ∼80 MHz oscillator repetition rates. The respective time delays of the individual laser pulses are scanned across a 12.5 ns window in a laboratory scan time of 10 ms, supporting a time delay resolution as fine as 15.6 fs. The repetition rate of the pump oscillator is synchronized to a Rb frequency standard via a PLL operating at the 12th harmonic of the oscillator repetition rate, achieving milliHertz (mHz) stability. We characterize the timing jitter of the system using an air-spaced etalon, an optical cross correlator, and the phase noise spectrum of the PLL. Spectroscopic applications of ASOPS-THz-TDS are demonstrated by measuring water vapor absorption lines from 0.55 to 3.35 THz and acetonitrile absorption lines from 0.13 to 1.39 THz in a short pathlength gas cell. With 70 min of data acquisition, a 50 dB signal-to-noise ratio is achieved. The achieved root-mean-square deviation is 14.6 MHz, with a mean deviation of 11.6 MHz, for the measured water line center frequencies as compared to the JPL molecular spectroscopy database. Further, with the same instrument and data acquisition hardware, we use the ability to control the repetition rate of the pump oscillator to enable THz frequency comb spectroscopy (THz-FCS). Here, a frequency comb with a tooth width of 5 MHz is generated and used to fully resolve the pure rotational spectrum of acetonitrile with Doppler-limited precision. The oscillator repetition rate stability achieved by our PLL lock circuits enables sub-MHz tooth width generation, if desired. This instrument provides unprecedented decade-spanning, tunable resolution, from 80 MHz down to sub-MHz, and heralds a new generation of gas-phase spectroscopic tools in the THz region

Heart rate reactivity is associated with future cognitive ability and cognitive change in a large community sample

The relationship between cardiovascular reactions to acute mental challenge in the laboratory and cognitive ability has received scant attention. The present study examined the association between reactivity and future cognitive ability. Heart rate and blood pressure reactions to a mental stress task were measured in 1647 participants comprising three distinct age cohorts. Cognitive ability was assessed using the Alice Heim-4 test of general intelligence and choice reaction time five and 12 years later. High heart rate reactivity was related to higher general intelligence scores and faster choice reaction times at both follow-ups. High heart rate reactivity was also associated with a smaller decline in cognitive ability between assessments. These associations were still evident following adjustment for a wide range of potentially confounding variables. The present results are consistent with the notion that high reactivity may not always be a maladaptive response and that low or blunted reactivity may also have negative corollaries

Squirrelpox virus: assessing prevalence, transmission and environmental degradation

Red squirrels (Sciurus vulgaris) declined in Great Britain and Ireland during the last century, due to habitat loss and the introduction of grey squirrels (Sciurus carolinensis), which competitively exclude the red squirrel and act as a reservoir for squirrelpox virus (SQPV). The disease is generally fatal to red squirrels and their ecological replacement by grey squirrels is up to 25 times faster where the virus is present. We aimed to determine: (1) the seropositivity and prevalence of SQPV DNA in the invasive and native species at a regional scale; (2) possible SQPV transmission routes; and, (3) virus degradation rates under differing environmental conditions. Grey (n = 208) and red (n = 40) squirrel blood and tissues were sampled. Enzyme-linked immunosorbent assay (ELISA) and quantitative real-time polymerase chain reaction (qPCR) techniques established seropositivity and viral DNA presence, respectively. Overall 8% of squirrels sampled (both species combined) had evidence of SQPV DNA in their tissues and 22% were in possession of antibodies. SQPV prevalence in sampled red squirrels was 2.5%. Viral loads were typically low in grey squirrels by comparison to red squirrels. There was a trend for a greater number of positive samples in spring and summer than in winter. Possible transmission routes were identified through the presence of viral DNA in faeces (red squirrels only), urine and ectoparasites (both species). Virus degradation analyses suggested that, after 30 days of exposure to six combinations of environments, there were more intact virus particles in scabs kept in warm (25°C) and dry conditions than in cooler (5 and 15°C) or wet conditions. We conclude that SQPV is present at low prevalence in invasive grey squirrel populations with a lower prevalence in native red squirrels. Virus transmission could occur through urine especially during warm dry summer conditions but, more notably, via ectoparasites, which are shared by both species