LemurFaceID: a face recognition system to facilitate individual identification of lemurs

Background: Long-term research of known individuals is critical for understanding the demographic and evolutionary processes that influence natural populations. Current methods for individual identification of many animals include capture and tagging techniques and/or researcher knowledge of natural variation in individual phenotypes. These methods can be costly, time-consuming, and may be impractical for larger-scale, populationlevel studies. Accordingly, for many animal lineages, long-term research projects are often limited to only a few taxa. Lemurs, a mammalian lineage endemic to Madagascar, are no exception. Long-term data needed to address evolutionary questions are lacking for many species. This is, at least in part, due to difficulties collecting consistent data on known individuals over long periods of time. Here, we present a new method for individual identification of lemurs (LemurFaceID). LemurFaceID is a computer-assisted facial recognition system that can be used to identify individual lemurs based on photographs. Results: LemurFaceID was developed using patch-wise Multiscale Local Binary Pattern features and modified facial image normalization techniques to reduce the effects of facial hair and variation in ambient lighting on identification. We trained and tested our system using images from wild red-bellied lemurs (Eulemur rubriventer) collected in Ranomafana National Park, Madagascar. Across 100 trials, with different partitions of training and test sets, we demonstrate that the LemurFaceID can achieve 98.7% ± 1.81% accuracy (using 2-query image fusion) in correctly identifying individual lemurs. Conclusions: Our results suggest that human facial recognition techniques can be modified for identification of individual lemurs based on variation in facial patterns. LemurFaceID was able to identify individual lemurs based on photographs of wild individuals with a relatively high degree of accuracy. This technology would remove many limitations of traditional methods for individual identification. Once optimized, our system can facilitate long-term research of known individuals by providing a rapid, cost-effective, and accurate method for individual identification

Automated identification of Monogeneans using digital image processing and K-nearest neighbour approaches.

BACKGROUND: Monogeneans are flatworms (Platyhelminthes) that are primarily found on gills and skin of fishes. Monogenean parasites have attachment appendages at their haptoral regions that help them to move about the body surface and feed on skin and gill debris. Haptoral attachment organs consist of sclerotized hard parts such as hooks, anchors and marginal hooks. Monogenean species are differentiated based on their haptoral bars, anchors, marginal hooks, reproductive parts' (male and female copulatory organs) morphological characters and soft anatomical parts. The complex structure of these diagnostic organs and also their overlapping in microscopic digital images are impediments for developing fully automated identification system for monogeneans (LNCS 7666:256-263, 2012), (ISDA; 457-462, 2011), (J Zoolog Syst Evol Res 52(2): 95-99. 2013;). In this study images of hard parts of the haptoral organs such as bars and anchors are used to develop a fully automated identification technique for monogenean species identification by implementing image processing techniques and machine learning methods. RESULT: Images of four monogenean species namely Sinodiplectanotrema malayanus, Trianchoratus pahangensis, Metahaliotrema mizellei and Metahaliotrema sp. (undescribed) were used to develop an automated technique for identification. K-nearest neighbour (KNN) was applied to classify the monogenean specimens based on the extracted features. 50% of the dataset was used for training and the other 50% was used as testing for system evaluation. Our approach demonstrated overall classification accuracy of 90%. In this study Leave One Out (LOO) cross validation is used for validation of our system and the accuracy is 91.25%. CONCLUSIONS: The methods presented in this study facilitate fast and accurate fully automated classification of monogeneans at the species level. In future studies more classes will be included in the model, the time to capture the monogenean images will be reduced and improvements in extraction and selection of features will be implemented

On the mechanism of response latencies in auditory nerve fibers

Despite the structural differences of the middle and inner ears, the latency pattern in auditory nerve fibers to an identical sound has been found similar across numerous species. Studies have shown the similarity in remarkable species with distinct cochleae or even without a basilar membrane. This stimulus-, neuron-, and species- independent similarity of latency cannot be simply explained by the concept of cochlear traveling waves that is generally accepted as the main cause of the neural latency pattern. An original concept of Fourier pattern is defined, intended to characterize a feature of temporal processing—specifically phase encoding—that is not readily apparent in more conventional analyses. The pattern is created by marking the first amplitude maximum for each sinusoid component of the stimulus, to encode phase information. The hypothesis is that the hearing organ serves as a running analyzer whose output reflects synchronization of auditory neural activity consistent with the Fourier pattern. A combined research of experimental, correlational and meta-analysis approaches is used to test the hypothesis. Manipulations included phase encoding and stimuli to test their effects on the predicted latency pattern. Animal studies in the literature using the same stimulus were then compared to determine the degree of relationship. The results show that each marking accounts for a large percentage of a corresponding peak latency in the peristimulus-time histogram. For each of the stimuli considered, the latency predicted by the Fourier pattern is highly correlated with the observed latency in the auditory nerve fiber of representative species. The results suggest that the hearing organ analyzes not only amplitude spectrum but also phase information in Fourier analysis, to distribute the specific spikes among auditory nerve fibers and within a single unit. This phase-encoding mechanism in Fourier analysis is proposed to be the common mechanism that, in the face of species differences in peripheral auditory hardware, accounts for the considerable similarities across species in their latency-by-frequency functions, in turn assuring optimal phase encoding across species. Also, the mechanism has the potential to improve phase encoding of cochlear implants

The diet of black-backed jackal (Canis Mesomelas) on two contrasting land-use types in the Eastern Cape Province, South Africa and the validation of a new analytical method of mammalian hair identification

Diet assessments are critical for understanding the foraging behaviour, habitat use and trophic separation of mammalian predators and are vital for gaining insight into how predators influence prey populations. The aim of this research was to qualitatively describe the diet of black-backed jackals (Canis mesomelas, Schreber 1775) using scat analysis on two contrasting land-use types in the Eastern Cape Province, South Africa. Scats were collected on a monthly basis from November 2009 to October 2010 from two game reserves (Great Fish River Reserve and Shamwari Private Game Reserve) and two neighbouring livestock farms. The relative frequency of occurrence of mammal hair (33 – 47 %) and vegetation (32 – 45%)dominated jackal diet throughout the year across the four study sites. Other important prey items included invertebrates (8 – 21 %) and fruit and seeds (3 – 11 %). Birds and reptiles constituted ≤ 2 % of the diet and were only recorded on the game reserves. Significant seasonal dietary shifts were observed on the game reserves but not on the farms. Fruit and seeds were significantly more frequent in the diet during autumn at Great Fish River Reserve and invertebrates were significantly less common in the diet during winter on both reserves. In addition, vegetation was significantly more common in the diet during winter at Shamwari Private Game Reserve. The significant temporal variation of certain prey items is testament to black-backed jackals being opportunistic generalists, foraging on those food items which are most abundant, accessible and energetically beneficial. Land-use type also influenced the diet of black-backed jackals with significantly more invertebrates and, fruit and seeds being recorded on the game reserves than on the farms. By contrast, significantly more mammal hair and vegetation were present in the diet on the farms compared with the game reserves. The mammalian component of the diet was dominated by ruminants and rodents on the game reserves and by ruminants and livestock on the farms. The presence of livestock in the diet of black-backed jackals on the farms highlights their potential impact on the livestock industry in the region and may assist farmers in determining which predators are responsible for stock loss. Previous approaches for identifying mammalian hairs from predator scats have utilised dichotomous keys and reference collections but these are often time-consuming and require a trained individual to carry out the identification. Thus, I also tested the efficacy of an automated pattern recognition programme (HairSnap) for identifying mammalian hairs from black-backed jackal scats. The overall accuracy of the programme was 38 % with black-backed jackal, Greater kudu (Tragelaphus strepsiceros) and striped polecat (Ictonyx striatus) hairs being accurately identified more often (70 – 80 %) than any other species tested. It is likely that both the size and species composition of the sample resulted in the poor accuracy of the programme. However, with the implementation of several improvement measures (e.g. adjustment of the algorithm) the programme may offer a superior, bias-free method of mammalian hair identification. The dietary information gathered here furthers our knowledge of the biology of the blackbacked jackals, especially in the locally important thicket biome. Moreover, understanding their foraging habits allows for more effective management of the species on both game reserves and farmlands. I recommend that future research should focus on quantitatively assessing the diet of black-backed jackals in the Eastern Cape Province and elsewhere. This will compliment the dietary description provided in this study and may offer a biologically more meaningful indication of the relative importance of the prey items

Diet and habitat of the little brown bat (Myotis lucifugus) in Interior and Northern Alaska

Thesis (M.S.) University of Alaska Fairbanks, 2016Little brown bats are sensitive to cold winters but consistent records of roosts in interior Alaska for 30 years indicate that the range of this species expands into the subarctic. We hypothesized that the little brown bat in interior and northern Alaska has adapted to high environmental demands by shifting foraging strategies. We analyzed guano to describe prey composition by microhistology, DNA analysis, stable isotope analysis, and image fragment recognition software. Alaskan bats consumed moths and flies, which was similar to the diet of southern conspecifics. However, bats in Alaska also consumed spiders. The stable isotopes of N and C in hair from bats in interior Alaskan bats were significantly different from bats in Yukon and coastal Alaska, which indicated the use of a separate habitat through summer. We used citizen science to collect reports of bats that ranged over most of Alaska and included sightings in the Arctic during autumn. Alaskan bats stored similar amounts of body fat to southern bats in autumn but unlike southern bats that migrate over 200 km, radio tracked bats in Alaska migrated short distances (<100km) to hibernacula in human structures. Expansion of the range of the little brown bat is apparently associated with a shift in foraging behavior to include gleaning of arthropods from surfaces. Overwintering at the extremely low air temperatures in interior Alaska is unlikely. Consequently, the persistence of bats in interior and northern Alaska may be related to consistent availability of human structures

Morphological and molecular approaches to characterise modifications relating to mammalian hairs in archaeological, paleontological and forensic contexts

Mammalian hair is readily shed and transferred to persons or objects during contact; this property renders hair as one of the most ubiquitous and prevalent evidence type encountered in forensic investigations and at ancient burial sites. The durability and stability of hair ensures their survival for millennia; their status as a privileged repository of viable genetic material consolidates their value as a biological substrate. The aims of this thesis are to showcase the wealth, and breadth, of information that may be gleaned from these unique structures and address the current problem regarding the mis-identification of animal hairs. Despite the similar appearance of human and animal hairs, the expertise required to accurately interpret their respective structures requires significantly different skill sets. Chapter Two in this thesis discusses the consequences of mis-identification of hair structures due to lack of competency or adequate training in regards to hair examiners and discusses some of the myths and misconceptions associated with microscopy of hairs. Hairs are resilient structures capable of surviving for millennia as exemplified by extinct megafauna hairs; however, they are not totally immune to deleterious effects of environmental insults or biodegradation. There is a paucity of morphological data available illustrating the deleterious effects of biological agents on hairs. This void is filled through the comprehensive review of biodegradation of hair in Chapter 3 which showcases, for the first time, a collective visual catalogue of the destructive effects caused by an elite group of biological agents. These effects were evident in hairs from prehistoric, ancient and modern human and animal hairs. During the course of this study hair morphologies were observed which challenged current paradigms in relation to their genesis. The results of the present study unequivocally demonstrate that hair structures, previously characterised as genetic in nature, are due to the effects of biodegradation. Furthermore, this body of work is the first to record that morphological characteristics previously ascribed to taphonomy (post-mortem insults), also occur in hairs from the living. The implications of the interpretation of hair structures in forensic investigations are discussed in greater detail in Chapter 3. Chapter four represents the first demonstration of the advantages of adopting a multidisciplinary approach to hair examination. This chapter presents a detailed microscopical audit of extinct megafauna hair that was the remains of a larger hair sample previously consumed in more destructive analyses (molecular analyses and radio carbon dating). One of the most significant morphological finds of this work was the presence of unusual structural features, not previously recorded, that may have been central to the survival of extinct megafauna. Lastly, Chapter Five introduces the concept of Next Generation Sequencing (NGS also referred to as massive parallel sequencing) to investigate the forensic potential of human hairs on the basis of transfer of their respective bacterial ‘profiles or signatures’. Taken together, this body of work presents fresh approaches to the manner in which mammalian hairs could be processed in the future and demonstrates the benefits of multi-disciplinary approaches to their examination. Bacterial DNA profiles, derived from human hair using NGS technologies, may prove to be a valuable future addition to the forensic molecular toolkit. Furthermore, this present study challenges current paradigms regarding the interpretation of microscopic post-mortem artifacts that occur on ancient and modern mammalian hairs

Aspects of spatiotemporal integration in bat sonar

Bat sonar is an active sense that is based on the common mammalian auditory system. Bats emit echolocation calls in the high frequency range and extract information about their surroundings by listening to the returning echoes. These echoes carry information, like spatial cues, about object location in the three-dimensional space (azimuth, elevation, and distance). Distance information, for example, is obtained from temporal cues as the interval between the emission of an echolocation call and the returning echo (echo delay). But echoes also carry information about spatial object properties like shape, orientation, or size (in terms of its height, width, and depth). To achieve a reliable internal representation of the environment, bats need to integrate spatial and temporal echo information. In this cumulative thesis different aspects of spatiotemporal integration in bat sonar were addressed, beginning with the perception and neural encoding of object size. Object width as size relevant dimension is encoded by the intensity of its echo. Additionally, the sonar aperture (the naturally co-varying spread of angles of incidence from which the echoes impinge on the ears) co-varies proportionally. In the first study, using a combined psychophysical and electrophysical approach (including the presentation of virtual objects), it was investigated which of both acoustic cues echolocating bats (Phyllostomus discolor) employ for the estimation of object width. Interestingly, the results showed that bats can discriminate object width by only using sonar-aperture information. This was reflected in the responses of a population of units in the auditory midbrain and cortex that responded strongest to echoes from objects with a specific sonar aperture, independent of variations in echo intensity. The study revealed that the sonar aperture is a behaviorally relevant and reliably encoded spatial perceptual cue for object size. It furthermore supported the theory that the mammalian central nervous system is principally aiming to find modality independent representation of spatial object properties. We therefore suggested that the sonar aperture, as an echo acoustic equivalent of the visual aperture (also referred to as the visual angle), could be one of these object properties. In the visual system object size is encoded by the visual aperture as the extent of the image on the retina. It depends on object distance that is not explicitly encoded. Thus, for reliable size perception at different distances, higher computational mechanisms are needed. This phenomenon is termed ‘size constancy’ or ‘size-distance invariance’ and is assumed to reflect an automatic re-scaling of visual aperture with perceived object distance. But in echolocating bats object width (sonar aperture) and object distance (echo delay) are accurately perceived and explicitly neurally encoded. In the second study we investigated whether bats show the ability to spontaneously combine spatial and temporal cues to determine absolute width information in terms of sonar size constancy (SSC). This was addressed by using the same setup and species as in the psychophysical approach of the first study. As a result SSC could not be verified as an important feature of sonar perception in bats. This lack of SSC could result from the bats relying on different modalities to extract size information at different distances. Alternatively, it is thinkable that familiarity with a behaviorally relevant, conspicuous object is required, as it was discussed for visual size constancy. But size constancy is found in many sensory modalities and more importantly, SSC was recently found in a blind human echolocator. It was discussed to be based on the same spatial and temporal cues as presented in our study. Thus, this topic should be readdressed in bats in a more natural context as size constancy could be a general mechanism for object normalization. As the spatiotemporal layout of the environment and the objects within changes with locomotion, in the third study the spatiotemporal integration in bat biosonar in a natural and naturalistic context was addressed. Trawling bats species hunt above water and capture fish or insects directly from or close to the surface. Here water acts as an acoustic mirror that can reduce clutter by reflecting sonar emissions away from the bats. However, objects on the water lead to echo enhancement. In a combined laboratory and field study we tested and quantified the effect of different surface types with different reflection properties (smooth and clutter surface) and object height on object detection and discrimination in the trawling bat species, Myotis daubentonii. The bats had to detect a mealworm presented above these different surfaces and discriminate it from an inedible PVC disk. At low heights above the clutter surface, the bats’ detection performance was worse than above a smooth surface. At a height of 50 cm, the surface structure had no influence on target detection. Above the clutter surface, object discrimination decreased with decreasing height. The study revealed different perceptual strategies that could allow efficient object detection and discrimination. When approaching objects above clutter, echolocation calls showed a significantly higher peak frequency, eventually suggesting a strategy for temporal separation of object echoes from clutter. Flight-path reconstruction showed that the bats attacked objects from below over water but from above over clutter. These results are consistent with the hypothesis that trawling bats exploit an echo-acoustic ground effect, in terms of a spatiotemporal integration of direct object reflections with indirect reflections from the water surface. It could lead to optimized prey-detection and discrimination not only for prey on the water but also above. Additionally, the bats could employ a precedence-like strategy to avoid misleading spatial cues that signal the wrong object elevation by using only the first and therewith direct echo for object localization

Morphological identification of animal hairs: Myths and misconceptions, possibilities and pitfalls

The examination of hair collected from crime scenes is an important and highly informative discipline relevant to many forensic investigations. However, the forensic identification of animal (non-human) hairs requires different skill sets and competencies to those required for human hair comparisons. The aim of this is paper is not only to highlight the intrinsic differences between forensic human hair comparison and forensic animal hair identification, but also discuss the utility and reliability of the two in the context of possibilities and pitfalls. It also addresses and dispels some of the more popular myths and misconceptions surrounding the microscopical examination of animal hairs. Furthermore, future directions of this discipline are explored through the proposal of recommendations for minimum standards for the morphological identification of animal hairs and the significance of the newly developed guidelines by SWGWILD is discussed

Circuit Neuroscience in Zebrafish

A central goal of modern neuroscience is to obtain a mechanistic understanding of higher brain functions under healthy and diseased conditions. Addressing this challenge requires rigorous experimental and theoretical analysis of neuronal circuits. Recent advances in optogenetics, high-resolution in vivo imaging, and reconstructions of synaptic wiring diagrams have created new opportunities to achieve this goal. To fully harness these methods, model organisms should allow for a combination of genetic and neurophysiological approaches in vivo. Moreover, the brain should be small in terms of neuron numbers and physical size. A promising vertebrate organism is the zebrafish because it is small, it is transparent at larval stages and it offers a wide range of genetic tools and advantages for neurophysiological approaches. Recent studies have highlighted the potential of zebrafish for exhaustive measurements of neuronal activity patterns, for manipulations of defined cell types in vivo and for studies of causal relationships between circuit function and behavior. In this article, we summarize background information on the zebrafish as a model in modern systems neuroscience and discuss recent results