Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an ...addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.
Yellowfin tuna (
Thunnus albacares
; YFT) is an apex marine predator inhabiting tropical and sub-tropical pelagic waters. It supports the second largest tuna fishery in the world. Here, we review the ...available literature on YFT to provide a detailed overview of the current knowledge of its biology, ecology, fisheries status, stock structure and management, at global scale. YFT are characterized by several peculiar anatomical and physiological traits that allow them to survive in the oligotrophic waters of the pelagic realm. They are opportunistic feeders, which allows fast growth and high reproductive outputs. Globally, YFT fisheries have expanded over the last century, progressively moving from coastal areas into the majority of sub-tropical and tropical waters. This expansion has led to a rapid increase in global commercial landings, which are predominantly harvested by industrial longline and purse seine fleets. For management purposes, YFT is divided into four stocks, each of which is currently managed by a separate tuna Regional Fisheries Management Organization. Our current understanding of YFT stock structure is, however, still uncertain, with conflicting evidence arising from genetic and tagging studies. There is, moreover, little information about their complex life-history traits or the interactions of YFT populations with spatio-temporally variable oceanographic conditions currently considered in stock assessments. What information is available, is often conflicting at the global scale. Finally, we suggest future research directions to manage this valuable resource with more biological realism and more sustainable procedures.
1. The temporal discharge patterns of auditory nerve fibers in Dial-anesthetized cats were studied in response to periodic complex acoustic waveforms that evoke pitches at their fundamental ...frequencies. Single-formant vowels, amplitude-modulated (AM) and quasi-frequency-modulated tones. AM noise, click trains, and other complex tones were utilized. Distributions of intervals between successive spikes ("1st-order intervals") and between both successive and nonsuccessive spikes ("all-order intervals") were computed from spike trains. Intervals from many fibers were pooled to estimate interspike interval distributions for the entire auditory nerve. Properties of these "pooled interspike interval distributions," such as the positions of interval peaks and their relative heights, were examined for correspondence to the psychophysical data on pitch frequency and pitch salience. 2. For a diverse set of complex stimuli and levels, the most frequent all-order interspike interval present in the pooled distribution corresponded to the pitch heard in psychophysical experiments. Pitch estimates based on pooled interval distributions (30-85 fibers, 100 stimulus presentations per fiber) were highly accurate (within 1%) for harmonic stimuli that produce strong pitches at 60 dB SPL. 3. Although the most frequent intervals in pooled all-order interval distributions were very stable with respect to sound intensity level (40, 60, and 80 dB total SPL), this was not necessarily the case for first-order interval distributions. Because the low pitches of complex tones are largely invariant with respect to level, pitches estimated from all-order interval distributions correspond better to perception. 4. Spectrally diverse stimuli that evoke similar low pitches produce pooled interval distributions with similar most-frequent intervals. This suggests that the pitch equivalence of these different stimuli could result from central auditory processing mechanisms that analyze interspike interval patterns. 5. Complex stimuli that evoke strong or "salient" pitches produce pooled interval distributions with high peak-to-mean ratios. Those stimuli that evoke weak pitches produce pooled interval distributions with low peak-to-mean ratios. 6. Pooled interspike interval distributions for stimuli consisting of low-frequency components generally resembled the short-time auto-correlation function of stimulus waveforms. Pooled interval distributions for stimuli consisting of high-frequency components resembled the short-time autocorrelation function of the waveform envelope. 7. Interval distributions in populations of neurons constitute a general, distributed means of encoding, transmitting, and representing information. Existence of a central processor capable of analyzing these interval patterns could provide a unified explanation for many different aspects of pitch perception.
Skates are characterised by conservative body morphology which hampers identification and leads to frequent taxonomic confusion and market mislabelling. Accurate specimen classification is crucial ...for reliable stock assessments and effective conservation plans, otherwise the risk of extinction could be unnoticed. The misclassification issue is evident for the genus Dipturus, distributed worldwide, from the continental shelf and slope to the deep sea. In this study, barcode cytochrome oxidase I gene (COI) sequences were used along with species delimitation and specimen assignment methods to improve taxonomy and zoogeography of species of conservation interest inhabiting the Atlantic Ocean and Mediterranean Sea. In this study, we provided new evidence of the occurence of D. nidarosiensis in the Central‐Western Mediterranean Sea and the lack of Atlantic‐Mediterranean genetic divergence. The Atlantic endangered species D. laevis and D. batis clustered together under the same molecular operational taxonomic unit (MOTU) with any delimitation methods used, while the assignment approach correctly discriminated specimens into the two species. These results provided evidence that the presence of the barcode gap is not an essential predictor of identification success, but the use of different approaches is crucially needed for specimen classification, especially when threshold‐ or tree‐based methods result less powerful. The analyses also showed how different putative, vulnerable, species dwelling across South‐Western Atlantic and South‐Eastern Pacific are frequently misidentified in public sequence repositories. Our study emphasised the limits associated to public databases, highlighting the urgency to verify and implement the information deposited therein in order to guarantee accurate species identification and thus effective conservation measures for deep‐sea skates.
Accurate specimen classification is crucial for reliable stock assessments and effective conservation plans, otherwise the risk of extinction could be unnoticed. The misclassification issue is evident for a range of taxa, especially those with conserved body morphology, such as skates belonging to the genus Dipturus. The joint use of COI barcode‐based methods as species delimitation and specimen assignment approaches could improve the accuracy of specimen identification and help to build curate reference libraries. This study also emphasizes the limits associated to public databases, highlighting the urgency to verify, update and implement the information deposited therein in order to guarantee correct identification and thus effective species conservation measures.
The genetic structure and population connectivity of the Mediterranean endemic speckled skate Raja polystigma were investigated in 10 population samples (N = 232) at 7 exonprimed nuclear ...microsatellites and at 3 mitochondrial DNA sequence markers. The phylogeographic and population genetic analyses revealed that R. polystigma in the western and central Mediterranean represents a near-panmictic population, with a subtle but significant mitochondrial divergence of the Adriatic deme. Nuclear genotypes revealed that 2.5% of the total individuals exhibited an admixed ancestry with the sibling species R. montagui (spotted ray). Individuals with admixed ancestry were detected along with purebred individuals in the Algerian, southern Tyrrhenian, Sicilian and Adriatic R. polystigma population samples, but they were absent or rare in Sardinian and northern Tyrrhenian ones. Since the 2 species co-occur in the southwestern Mediterranean, we suggested that this area may act as a secondary hybrid zone.
A roadmap for the study of conscious audition and its neural basis Dykstra, Andrew R.; Cariani, Peter A.; Gutschalk, Alexander
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
02/2017, Volume:
372, Issue:
1714
Journal Article
Peer reviewed
Open access
How and which aspects of neural activity give rise to subjective perceptual experience—i.e. conscious perception—is a fundamental question of neuroscience. To date, the vast majority of work ...concerning this question has come from vision, raising the issue of generalizability of prominent resulting theories. However, recent work has begun to shed light on the neural processes subserving conscious perception in other modalities, particularly audition. Here, we outline a roadmap for the future study of conscious auditory perception and its neural basis, paying particular attention to how conscious perception emerges (and of which elements or groups of elements) in complex auditory scenes. We begin by discussing the functional role of the auditory system, particularly as it pertains to conscious perception. Next, we ask: what are the phenomena that need to be explained by a theory of conscious auditory perception? After surveying the available literature for candidate neural correlates, we end by considering the implications that such results have for a general theory of conscious perception as well as prominent outstanding questions and what approaches/techniques can best be used to address them.
This article is part of the themed issue ‘Auditory and visual scene analysis’.
1. The neural correlates of low pitches produced by complex tones were studied by analyzing temporal discharge patterns of auditory nerve fibers in Dial-anesthetized cats. In the previous paper it ...was observed that, for harmonic stimuli, the most frequent interspike interval present in the population of auditory nerve fibers always corresponded to the perceived pitch (predominant interval hypothesis). The fraction of these most frequent intervals relative to the total number of intervals qualitatively corresponded to strength (salience) of the low pitches that are heard. 2. This paper addresses the neural correlates of stimuli that produce more complex patterns of pitch judgments, such as shifts in pitch and multiple pitches. Correlates of pitch shift and pitch ambiguity were investigated with the use of harmonic and inharmonic amplitude-modulated (AM) tones varying either in carrier frequency or modulation frequency. Pitches estimated from the pooled interval distributions showed shifts corresponding to "the first effect of pitch shift" (de Boer's rule) that is observed psychophysically. Pooled interval distributions in response to inharmonic stimulus segments showed multiple maxima corresponding to the multiple pitches heard by human listeners (pitch ambiguity). 3. AM and quasi-frequency-modulated tones with low carrier frequencies produce very similar patterns of pitch judgments, despite great differences in their phase spectra and waveform envelopes. Pitches estimated from pooled interval distributions were remarkably similar for the two kinds of stimuli, consistent with the psychophysically observed phase invariance of pitches produced by sets of low-frequency components. 4. Trains of clicks having uniform and alternating polarities were used to investigate the relation between pitches associated with periodicity and those associated with click rate. For unipolar click trains, where periodicity and rate coincide, physiologically estimated pitches closely follow the fundamental period. This corresponds to the pitch at the fundamental frequency (F0) that is heard. For alternating click trains, where rate and periodicity do not coincide, physiologically estimated pitches always closely followed the fundamental period. Although these pitch estimates corresponded to periodicity pitches that are heard for F0s > 150 Hz, they did not correspond to the rate pitches that are heard for F0s < 150 Hz. The predominant interval hypothesis thus failed to predict rate pitch. 5. When alternating-polarity click trains are high-pass filtered, rate pitches are strengthened and can also be heard at F0s > 150 Hz. Pitches for high-pass-filtered alternating click trains were estimated from pooled responses of fibers with characteristic frequencies (CFs) > 2 kHz. Roughly equal numbers of intervals at 1/rate and 1/F0 were found for all F0s studied, from 80 to 160 Hz, producing pitch estimates consistent with the rate pitches that are heard after high-pass filtering. The existence region for rate pitch also coincided with the presence of clear periodicities related to the click rate in pooled peristimulus time histograms. These periodicities were strongest for ensembles of fibers with CFs > 2 kHz, where there is widespread synchrony of discharges across many fibers. 6. The "dominance region for pitch" was studied with the use of two harmonic complexes consisting of harmonics 3-5 of one F0 and harmonics 6-12 of another fundamental 20% higher in frequency. When the complexes were presented individually, pitch estimates were always close to the fundamental of the complex. When the complexes were presented concurrently, pitch estimates always followed the fundamental of harmonics 3-5 for F0s of 150-480 Hz. For F0s of 125-150 Hz, pitch estimates followed one or the other fundamental, and for F0s < 125 Hz, pitch estimates followed the fundamental of harmonics 6-12. (ABSTRACT TRUNCATED)
The actual occurrence of Squalus megalops in the Mediterranean Sea has recently been questioned. Several research works which sought to assess available morphological and meristic features that ...differentiate S. megalops from other Squalus species in the Mediterranean Sea, revealed poor discriminatory power and high variability of the assessed characters, especially when comparing S. megalops and S. blainville. The application of molecular tools does not support the presence of S. megalops. In the present study, we screened spurdog species from the Strait of Sicily using a molecular taxonomy approach based on two mitochondrial DNA markers and we report the occurrence of two Squalus lineages characterizing specimens collected from the stretch of sea between Tunisia, southern Sicily, Malta and Libya. The results support the hypothesis that a common species, S. blainville, currently inhabits the Mediterranean Sea, while a second and rare species is probably an occasional visitor with high morphological similarity to the S. megalops and S. blainville but is genetically distinct from both. Within this perspective, the occurrence of S. megalops in the Mediterranean Sea is not confirmed and our study highlights the taxonomic uncertainties in relation to the occurrence and distribution of Squalus species in this region. We encourage the establishment of a coordinated international effort to implement a comprehensive and integrated taxonomic assessment on this genus which represents an irreplaceable component of the biodiversity of the area.
Chondrichthyan egg cases are important elements for species-specific identification and also provide a valuable aid in determining a species spatial distribution, as well as for defining spawning ...areas. Considering the absence of a general key for the identification of the egg cases of the Mediterranean Chondrichthyes, this work aims to fill this gap by presenting a species-specific key based on morphological features of the egg case. The key was developed primarily analysing fresh egg cases dissected from the oviduct, egg cases collected from the seabed or found dried lying on the seashore, after species confirmation by DNA analysis. Original data were integrated with information scrutinized from literature. In order to improve species identification, a protocol for the standardized acquisition of morpho-biometric and meristic features is also provided as a pre-requisite for the appropriate use of the identification key. The total width and length included the horns, when they are not broken, are the parameters that best explain the assignment of the egg case to a specific species.
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