Repeated intercontinental migrations and recurring hybridizations characterise the evolutionary history of yew (Taxus L.).

The genus Taxus (Taxaceae) consists of 16 genetically well-defined lineages that are predominantly distributed across the Northern hemisphere. We investigated its biogeographic origin and evolutionary history by sampling 13 chloroplast gene sequences, the nuclear internal transcribed spacers (ITS) and NEEDLY sequences for all 16 lineages. We applied Maximum Parsimony and Bayesian Inference analyses to infer their phylogenetic relationships, time-calibrated phylogenies using BEAST and inferred the ancestral area of occupancy with BioGeoBEARS. We found strong evidence for the hybrid origin of three lineages and dated these events to a rather narrow time window of 6.8-4.9 million years ago (Mya). The dated phylogenies inferred an Upper Cretaceous origin of the genus, with the extant lineages diversifying in North America much later during the Oligocene/early Miocene. Repeated migrations via the Bering land bridge to Eurasia and back were further inferred, with the return to North America as a possible result of vicariance. The diversification in Eurasia (from ~8 Mya onwards) coincided with the orogeny of the Hengduan Mountains, the intensification of the East Asian summer monsoon and the occupancy of ecological niches by lineages that experienced secondary contacts and hybridizations in the Hengduan Mountains and Qinling Mountain, especially around the Sichuan basin. We provide a hypothesis for the evolution of extant lineages of Taxus, a genus with an old and complex evolutionary history. The study highlights that the history of complex species can be unravelled with a careful dissection of phylogenetic signals.

Spatial Processing Is Frequency Specific in Auditory Cortex But Not in the Midbrain.

The cochlea behaves like a bank of band-pass filters, segregating information into different frequency channels. Some aspects of perception reflect processing within individual channels, but others involve the integration of information across them. One instance of this is sound localization, which improves with increasing bandwidth. The processing of binaural cues for sound location has been studied extensively. However, although the advantage conferred by bandwidth is clear, we currently know little about how this additional information is combined to form our percept of space. We investigated the ability of cells in the auditory system of guinea pigs to compare interaural level differences (ILDs), a key localization cue, between tones of disparate frequencies in each ear. Cells in auditory cortex believed to be integral to ILD processing (excitatory from one ear, inhibitory from the other: EI cells) compare ILDs separately over restricted frequency ranges which are not consistent with their monaural tuning. In contrast, cells that are excitatory from both ears (EE cells) show no evidence of frequency-specific processing. Both cell types are explained by a model in which ILDs are computed within separate frequency channels and subsequently combined in a single cortical cell. Interestingly, ILD processing in all inferior colliculus cell types (EE and EI) is largely consistent with processing within single, matched-frequency channels from each ear. Our data suggest a clear constraint on the way that localization cues are integrated: cortical ILD tuning to broadband sounds is a composite of separate, frequency-specific, binaurally sensitive channels. This frequency-specific processing appears after the level of the midbrain.SIGNIFICANCE STATEMENT For some sensory modalities (e.g., somatosensation, vision), the spatial arrangement of the outside world is inherited by the brain from the periphery. The auditory periphery is arranged spatially by frequency, not spatial location. Therefore, our auditory perception of location must be synthesized from physical cues in separate frequency channels. There are multiple cues (e.g., timing, level, spectral cues), but even single cues (e.g., level differences) are frequency dependent. The synthesis of location must account for this frequency dependence, but it is not known how this might occur. Here, we investigated how interaural-level differences are combined across frequency along the ascending auditory system. We found that the integration in auditory cortex preserves the independence of the different-level cues in different frequency regions.

Hidden in plain view: Cryptic diversity in the emblematic Araucaria of New Caledonia.

PREMISE OF THE STUDY: Cryptic species represent a conservation challenge, because distributions and threats cannot be accurately assessed until species are recognized and defined. Cryptic species are common in diminutive and morphologically simple organisms, but are rare in charismatic and/or highly visible groups such as conifers. New Caledonia, a small island in the southern Pacific is a hotspot of diversity for the emblematic conifer genus Araucaria (Araucariaceae, Monkey Puzzle trees) where 13 of the 19 recognized species are endemic. METHODS: We sampled across the entire geographical distribution of two closely related species (Araucaria rulei and A. muelleri) and screened them for genetic variation at 12 nuclear and 14 plastid microsatellites and one plastid minisatellite; a subset of the samples was also examined using leaf morphometrics. KEY RESULTS: The genetic data show that populations of the endangered A. muelleri fall into two clearly distinct genetic groups: one corresponding to montane populations, the other corresponding to trees from lower elevation populations from around the Goro plateau. These Goro plateau populations are more closely related to A. rulei, but are sufficiently genetically and morphological distinct to warrant recognition as a new species. CONCLUSIONS: Our study shows the presence of a previously unrecognized species in this flagship group, and that A. muelleri has 30% fewer individuals than previously thought. Combined, this clarification of species diversity and distributions provides important information to aid conservation planning for New Caledonian Araucaria.

Utilising temporal signal features in adverse noise conditions: Detection, estimation, and the reassigned spectrogram.

Visual displays in passive sonar based on the Fourier spectrogram are underpinned by detection models that rely on signal and noise power statistics. Time-frequency representations specialised for sparse signals achieve a sharper signal representation, either by reassigning signal energy based on temporal structure or by conveying temporal structure directly. However, temporal representations involve nonlinear transformations that make it difficult to reason about how they respond to additive noise. This article analyses the effect of noise on temporal fine structure measurements such as zero crossings and instantaneous frequency. Detectors that rely on zero crossing intervals, intervals and peak amplitudes, and instantaneous frequency measurements are developed, and evaluated for the detection of a sinusoid in Gaussian noise, using the power detector as a baseline. Detectors that rely on fine structure outperform the power detector under certain circumstances; and detectors that rely on both fine structure and power measurements are superior. Reassigned spectrograms assume that the statistics used to reassign energy are reliable, but the derivation of the fine structure detectors indicates the opposite. The article closes by proposing and demonstrating the concept of a doubly reassigned spectrogram, wherein temporal measurements are reassigned according to a statistical model of the noise background.

Towards a comprehensive phylogeny of the large temperate genus Pedicularis (Orobanchaceae), with an emphasis on species from the Himalaya-Hengduan Mountains.

BACKGROUND: Striking interspecific variations in floral traits of the large temperate genus Pedicularis have given rise to controversies concerning infra-generic classifications. To date, phylogenetic relationships within the genus have not been well resolved. The main goal of this study is to construct a backbone phylogeny of Pedicularis, with extensive sampling of species from the Himalaya-Hengduan Mountains. Phylogenetic analyses included 257 species, representing all 13 informal groups and 104 out of 130 series in the classification system of Tsoong, using sequences of the nuclear ribosomal internal transcribed spacer (nrITS) and three plastid regions (matK, rbcL and trnL-F). Bayesian inference and maximum likelihood methods were applied in separate and combined analyses of these datasets. RESULTS: Thirteen major clades are resolved with strong support, although the backbone of the tree is poorly resolved. There is little consensus between the phylogenetic tree and Tsoong's classification of Pedicularis. Only two of the 13 groups (15.4 %), and 19 of the 56 series (33.9 %) with more than one sampled species were found to be strictly monophyletic. Most opposite-/whorled-leaved species fall into a single clade, i.e. clade 1, while alternate leaves species occur in the remaining 12 clades. Excluding the widespread P. verticillata in clade 1, species from Europe and North America fall into clades 6-8. CONCLUSIONS: Our results suggest that combinations of morphological and geographic characters associated with strongly supported clades are needed to elucidate a comprehensive global phylogeny of Pedicularis. Alternate leaves are inferred to be plesiomorphic in Pedicularis, with multiple transitions to opposite/whorled phyllotaxy. Alternate-leaved species show high diversity in plant habit and floral forms. In the Himalaya-Hengduan Mountains, geographical barriers may have facilitated diversification of species with long corolla tubes, and the reproductive advantages of beakless galeas in opposite-/whorled-leaved species may boost speciation at high altitude.

Decision criterion dynamics in animals performing an auditory detection task.

Classical signal detection theory attributes bias in perceptual decisions to a threshold criterion, against which sensory excitation is compared. The optimal criterion setting depends on the signal level, which may vary over time, and about which the subject is naïve. Consequently, the subject must optimise its threshold by responding appropriately to feedback. Here a series of experiments was conducted, and a computational model applied, to determine how the decision bias of the ferret in an auditory signal detection task tracks changes in the stimulus level. The time scales of criterion dynamics were investigated by means of a yes-no signal-in-noise detection task, in which trials were grouped into blocks that alternately contained easy- and hard-to-detect signals. The responses of the ferrets implied both long- and short-term criterion dynamics. The animals exhibited a bias in favour of responding "yes" during blocks of harder trials, and vice versa. Moreover, the outcome of each single trial had a strong influence on the decision at the next trial. We demonstrate that the single-trial and block-level changes in bias are a manifestation of the same criterion update policy by fitting a model, in which the criterion is shifted by fixed amounts according to the outcome of the previous trial and decays strongly towards a resting value. The apparent block-level stabilisation of bias arises as the probabilities of outcomes and shifts on single trials mutually interact to establish equilibrium. To gain an intuition into how stable criterion distributions arise from specific parameter sets we develop a Markov model which accounts for the dynamic effects of criterion shifts. Our approach provides a framework for investigating the dynamics of decisions at different timescales in other species (e.g., humans) and in other psychological domains (e.g., vision, memory).

Evolutionary diversification of new Caledonian Araucaria.

New Caledonia is a global biodiversity hotspot. Hypotheses for its biotic richness suggest either that the island is a 'museum' for an old Gondwana biota or alternatively it has developed following relatively recent long distance dispersal and in situ radiation. The conifer genus Araucaria (Araucariaceae) comprises 19 species globally with 13 endemic to this island. With a typically Gondwanan distribution, Araucaria is particularly well suited to testing alternative biogeographic hypotheses concerning the origins of New Caledonian biota. We derived phylogenetic estimates using 11 plastid and rDNA ITS2 sequence data for a complete sampling of Araucaria (including multiple accessions of each of the 13 New Caledonian Araucaria species). In addition, we developed a dataset comprising 4 plastid regions for a wider taxon sample to facilitate fossil based molecular dating. Following statistical analyses to identify a credible and internally consistent set of fossil constraints, divergence times estimated using a Bayesian relaxed clock approach were contrasted with geological scenarios to explore the biogeographic history of Araucaria. The phylogenetic data resolve relationships within Araucariaceae and among the main lineages in Araucaria, but provide limited resolution within the monophyletic New Caledonian species group. Divergence time estimates suggest a Late Cretaceous-Cenozoic radiation of extant Araucaria and a Neogene radiation of the New Caledonian lineage. A molecular timescale for the evolution of Araucariaceae supports a relatively recent radiation, and suggests that earlier (pre-Cenozoic) fossil types assigned to Araucaria may have affinities elsewhere in Araucariaceae. While additional data will be required to adequately resolve relationships among the New Caledonian species, their recent origin is consistent with overwater dispersal following Eocene emersion of New Caledonia but is too old to support a single dispersal from Australia to Norfolk Island for the radiation of the Pacific Araucaria sect. Eutacta clade.

Stable individual characteristics in the perception of multiple embedded patterns in multistable auditory stimuli.

The ability of the auditory system to parse complex scenes into component objects in order to extract information from the environment is very robust, yet the processing principles underlying this ability are still not well understood. This study was designed to investigate the proposal that the auditory system constructs multiple interpretations of the acoustic scene in parallel, based on the finding that when listening to a long repetitive sequence listeners report switching between different perceptual organizations. Using the "ABA-" auditory streaming paradigm we trained listeners until they could reliably recognize all possible embedded patterns of length four which could in principle be extracted from the sequence, and in a series of test sessions investigated their spontaneous reports of those patterns. With the training allowing them to identify and mark a wider variety of possible patterns, participants spontaneously reported many more patterns than the ones traditionally assumed (Integrated vs. Segregated). Despite receiving consistent training and despite the apparent randomness of perceptual switching, we found individual switching patterns were idiosyncratic; i.e., the perceptual switching patterns of each participant were more similar to their own switching patterns in different sessions than to those of other participants. These individual differences were found to be preserved even between test sessions held a year after the initial experiment. Our results support the idea that the auditory system attempts to extract an exhaustive set of embedded patterns which can be used to generate expectations of future events and which by competing for dominance give rise to (changing) perceptual awareness, with the characteristics of pattern discovery and perceptual competition having a strong idiosyncratic component. Perceptual multistability thus provides a means for characterizing both general mechanisms and individual differences in human perception.

Predictive regularity representations in violation detection and auditory stream segregation: from conceptual to computational models.

Predictive accounts of perception have received increasing attention in the past 20 years. Detecting violations of auditory regularities, as reflected by the Mismatch Negativity (MMN) auditory event-related potential, is amongst the phenomena seamlessly fitting this approach. Largely based on the MMN literature, we propose a psychological conceptual framework called the Auditory Event Representation System (AERS), which is based on the assumption that auditory regularity violation detection and the formation of auditory perceptual objects are based on the same predictive regularity representations. Based on this notion, a computational model of auditory stream segregation, called CHAINS, has been developed. In CHAINS, the auditory sensory event representation of each incoming sound is considered for being the continuation of likely combinations of the preceding sounds in the sequence, thus providing alternative interpretations of the auditory input. Detecting repeating patterns allows predicting upcoming sound events, thus providing a test and potential support for the corresponding interpretation. Alternative interpretations continuously compete for perceptual dominance. In this paper, we briefly describe AERS and deduce some general constraints from this conceptual model. We then go on to illustrate how these constraints are computationally specified in CHAINS.

Modelling the emergence and dynamics of perceptual organisation in auditory streaming.

Many sound sources can only be recognised from the pattern of sounds they emit, and not from the individual sound events that make up their emission sequences. Auditory scene analysis addresses the difficult task of interpreting the sound world in terms of an unknown number of discrete sound sources (causes) with possibly overlapping signals, and therefore of associating each event with the appropriate source. There are potentially many different ways in which incoming events can be assigned to different causes, which means that the auditory system has to choose between them. This problem has been studied for many years using the auditory streaming paradigm, and recently it has become apparent that instead of making one fixed perceptual decision, given sufficient time, auditory perception switches back and forth between the alternatives-a phenomenon known as perceptual bi- or multi-stability. We propose a new model of auditory scene analysis at the core of which is a process that seeks to discover predictable patterns in the ongoing sound sequence. Representations of predictable fragments are created on the fly, and are maintained, strengthened or weakened on the basis of their predictive success, and conflict with other representations. Auditory perceptual organisation emerges spontaneously from the nature of the competition between these representations. We present detailed comparisons between the model simulations and data from an auditory streaming experiment, and show that the model accounts for many important findings, including: the emergence of, and switching between, alternative organisations; the influence of stimulus parameters on perceptual dominance, switching rate and perceptual phase durations; and the build-up of auditory streaming. The principal contribution of the model is to show that a two-stage process of pattern discovery and competition between incompatible patterns can account for both the contents (perceptual organisations) and the dynamics of human perception in auditory streaming.

Distribution of living Cupressaceae reflects the breakup of Pangea.

Most extant genus-level radiations in gymnosperms are of Oligocene age or younger, reflecting widespread extinction during climate cooling at the Oligocene/Miocene boundary [∼23 million years ago (Ma)]. Recent biogeographic studies have revealed many instances of long-distance dispersal in gymnosperms as well as in angiosperms. Acting together, extinction and long-distance dispersal are likely to erase historical biogeographic signals. Notwithstanding this problem, we show that phylogenetic relationships in the gymnosperm family Cupressaceae (162 species, 32 genera) exhibit patterns expected from the Jurassic/Cretaceous breakup of Pangea. A phylogeny was generated for 122 representatives covering all genera, using up to 10,000 nucleotides of plastid, mitochondrial, and nuclear sequence per species. Relying on 16 fossil calibration points and three molecular dating methods, we show that Cupressaceae originated during the Triassic, when Pangea was intact. Vicariance between the two subfamilies, the Laurasian Cupressoideae and the Gondwanan Callitroideae, occurred around 153 Ma (124-183 Ma), when Gondwana and Laurasia were separating. Three further intercontinental disjunctions involving the Northern and Southern Hemisphere are coincidental with or immediately followed the breakup of Pangea.

Characterising switching behaviour in perceptual multi-stability.

When people experience an unchanging sensory input for a long period of time, their perception tends to switch stochastically and unavoidably between alternative interpretations of the sensation; a phenomenon known as perceptual bi-stability or multi-stability. The huge variability in the experimental data obtained in such paradigms makes it difficult to distinguish typical patterns of behaviour, or to identify differences between switching patterns. Here we propose a new approach to characterising switching behaviour based upon the extraction of transition matrices from the data, which provide a compact representation that is well-understood mathematically. On the basis of this representation we can characterise patterns of perceptual switching, visualise and simulate typical switching patterns, and calculate the likelihood of observing a particular switching pattern. The proposed method can support comparisons between different observers, experimental conditions and even experiments. We demonstrate the insights offered by this approach using examples from our experiments investigating multi-stability in auditory streaming. However, the methodology is generic and thus widely applicable in studies of multi-stability in any domain.

Multistability in auditory stream segregation: a predictive coding view.

Auditory stream segregation involves linking temporally separate acoustic events into one or more coherent sequences. For any non-trivial sequence of sounds, many alternative descriptions can be formed, only one or very few of which emerge in awareness at any time. Evidence from studies showing bi-/multistability in auditory streaming suggest that some, perhaps many of the alternative descriptions are represented in the brain in parallel and that they continuously vie for conscious perception. Here, based on a predictive coding view, we consider the nature of these sound representations and how they compete with each other. Predictive processing helps to maintain perceptual stability by signalling the continuation of previously established patterns as well as the emergence of new sound sources. It also provides a measure of how well each of the competing representations describes the current acoustic scene. This account of auditory stream segregation has been tested on perceptual data obtained in the auditory streaming paradigm.

Characterising stimulus-specific adaptation using a multi-layer field model.

The response of an auditory neuron to a tone is often affected by the context in which the tone appears. For example, when measuring the response to a random sequence of tones, frequencies that appear rarely elicit a greater number of spikes than those that appear often. This phenomenon is called stimulus-specific adaptation (SSA). This article presents a neural field model in which SSA arises through selective adaptation to the frequently-occurring inputs. Formulating the network as a field model allows one to obtain an analytical expression for the expected response of a simple two-layer model to tones in a random sequence. The sequences of stimuli used in SSA experiments contain hundreds-and sometimes thousands-of tones, and these experiments routinely measure the response to many such sequences. A conventional neural network model (e.g., integrate-and-fire) would require numerical integration over long time periods to obtain results. Consequently, a field model that offers an immediate, analytical solution for a given input sequence is helpful. Two routes to obtaining this solution are discussed. The first involves the convolution of two closed-form expressions; the second relies on a series of approximations involving Gaussian curves. The purpose of the paper is to describe the model, to develop the approximations that allow an analytical solution, and finally, to comment on the output of the model in light of the SSA results published in the physiology literature. This article is part of a Special Issue entitled "Neural Coding".

A neurocomputational model of stimulus-specific adaptation to oddball and Markov sequences.

Stimulus-specific adaptation (SSA) occurs when the spike rate of a neuron decreases with repetitions of the same stimulus, but recovers when a different stimulus is presented. It has been suggested that SSA in single auditory neurons may provide information to change detection mechanisms evident at other scales (e.g., mismatch negativity in the event related potential), and participate in the control of attention and the formation of auditory streams. This article presents a spiking-neuron model that accounts for SSA in terms of the convergence of depressing synapses that convey feature-specific inputs. The model is anatomically plausible, comprising just a few homogeneously connected populations, and does not require organised feature maps. The model is calibrated to match the SSA measured in the cortex of the awake rat, as reported in one study. The effect of frequency separation, deviant probability, repetition rate and duration upon SSA are investigated. With the same parameter set, the model generates responses consistent with a wide range of published data obtained in other auditory regions using other stimulus configurations, such as block, sequential and random stimuli. A new stimulus paradigm is introduced, which generalises the oddball concept to Markov chains, allowing the experimenter to vary the tone probabilities and the rate of switching independently. The model predicts greater SSA for higher rates of switching. Finally, the issue of whether rarity or novelty elicits SSA is addressed by comparing the responses of the model to deviants in the context of a sequence of a single standard or many standards. The results support the view that synaptic adaptation alone can explain almost all aspects of SSA reported to date, including its purported novelty component, and that non-trivial networks of depressing synapses can intensify this novelty response.

Emergent feature sensitivity in a model of the auditory thalamocortical system.

If, as is widely believed, perception is based upon the responses of neurons that are tuned to stimulus features, then precisely what features are encoded and how do neurons in the system come to be sensitive to those features? Here we show differential responses to ripple stimuli can arise through exposure to formative stimuli in a recurrently connected model of the thalamocortical system which exhibits delays, lateral and recurrent connections, and learning in the form of spike timing dependent plasticity.

Abstract stimulus-specific adaptation models.

Many neurons that initially respond to a stimulus stop responding if the stimulus is presented repeatedly but recover their response if a different stimulus is presented. This phenomenon is referred to as stimulus-specific adaptation (SSA). SSA has been investigated extensively using oddball experiments, which measure the responses of a neuron to sequences of stimuli. Neurons that exhibit SSA respond less vigorously to common stimuli, and the metric typically used to quantify this difference is the SSA index (SI). This article presents the first detailed analysis of the SI metric by examining the question: How should a system (e.g., a neuron) respond to stochastic input if it is to maximize the SI of its output? Questions like this one are particularly relevant to those wishing to construct computational models of SSA. If an artificial neural network receives stimulus information at a particular rate and must respond within a fixed time, what is the highest SI one can reasonably expect? We demonstrate that the optimum, average SI is constrained by the information in the input source, the length and encoding of the memory, and the assumptions concerning how the task is decomposed.

Species separation of Taxus baccata, T. canadensis, and T. cuspidata (Taxaceae) and origins of their reputed hybrids inferred from RAPD and cpDNA data.

Species delimitation in Taxus (Taxaceae) has been controversial due to high levels of phenotypic plasticity. Reputed hybrids between species have been questioned due to the original crosses' accidental nature and the uncertainty regarding the parent species' distinctness. In this study 19 samples from three species (T. baccata, T. canadensis, T. cuspidata) and 31 from putative hybrids (T. × hunnewelliana, T. × media) have been DNA-fingerprinted using RAPDs and characterized for their respective chloroplast genotype using restriction digestions of polymerase chain reaction- (PCR) amplified trnL-F fragments. All samples showed unique RAPD banding profiles. Twenty-one RAPD bands were species-specific; the presence of these bands in the putative hybrids confirmed the hybrid origin and parentage suspected from morphological studies (T. cuspidata × T. canadensis = T. × hunnewelliana, T. baccata × T. cuspidata = T. × media). Principal coordinates analysis (PCO) and unweighted pair-group method algorithm (UPGMA) analyses of RAPD bands clearly separated the species, indicating that they belong to discrete genetic stocks and supporting their individual species status. The two hybrid groups also clustered discretely. Chloroplast typing confirmed the direction of crosses. The data further suggested that repeated reciprocal crossings occurred in the production of the hybrid cultivars.