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Biology subjects

Bowie, R. C. K.

Publications and source records attributed to Bowie, R. C. K..

4 recordsLinked to original sources

A comparison of visual features used by humans and machines to classify wildlife

In our quest to develop more intelligent machines, knowledge of the visual features used by machines to classify objects shall be helpful. The current state of the art in training machines to classify wildlife species from camera-trap data is to employ convolutional neural networks (CNN) encoded within deep learning algorithms. Here we report on results obtained in training a CNN to classify 20 African wildlife species with an overall accuracy of 87.5% from a dataset containing 111,467 images. We then used a gradient-weighted class-activation-mapping (Grad-CAM) procedure to extract the most salient pixels in the final convolution layer. We show that these pixels highlight features in particular images that are in most, but not all, cases similar to those used to train humans to identify these species. Further, we used mutual information methods to identify the neurons in the final convolution layer that consistently respond most strongly across a set of images of one particular species, and we then interpret the features in the image where the strongest responses occur. We also used hierarchical clustering of feature vectors (i.e., the state of the final fully-connected layer in the CNN) associated with each image to produce a visual similarity dendrogram of identified species. Finally, we evaluated how images that were not part of the training set fell within our dendrogram when these images were one of the 20 species \"known\" to our CNN in contrast to where they fell when these images were \"unknown\" to our CNN.

ecology

Whole-genome analysis of introgression between the spotted owl and barred owl (Strix occidentalis and Strix varia, respectively; Aves: Strigidae) in western North America

As the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix varia and S. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of western S. varia that suggested admixture with S. occidentalis appear unrelated to S. occidentalis ancestry and may instead reflect local selection.

genomics

Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California

We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale assessment of the genome-wide nucleotide diversity across S. occidentalis populations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all California S. occidentalis populations. We found no evidence of genetic differentiation between northern spotted owl (S. o. caurina) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl (S. o. occidentalis) than between populations of S. o. occidentalis and S. o. caurina in northern California. The San Diego County S. o. occidentalis population was substantially diverged from the other three S. occidentalis populations. These whole-genome data support a pattern of isolation-by-distance across spotted owl populations in California, rather than elevated differentiation between currently recognized subspecies.

genomics

Taxonomy, phylogeny and biogeography of African spurfowls (Galliformes, Phasianidae, Coturnicinae, Pternistis spp.)

During much of the 20th Century, partridge/quail-like, Afro-Asian phasianine birds referred to commonly as African spurfowls, francolins and/or partridges had a tortuous taxonomic history. Because of striking autapomorphic differences in plumage, vocalizations and ecology in some of these taxa, as many as nine genera and nearly 200 clinal and/or idiosyncratic subspecies, embedded within a polyphyletic Perdicinae, were recognized. In 1963, two clades, 28 francolin and spurfowl species (fisante in Afrikaans) and 13 Afro-Asiatic francolins and partridges (patryse in Afrikaans), were combined into a single genus (Francolinus) - the largest within the Galliformes - comprising about 100 subspecies. Furthermore, fisante and patryse were partitioned into several unnamed \"Groups\" and four \"Unplaced\" species. Here, we use morphological, behavioural and DNA evidence to produce: a comprehensive revision of the taxonomy and phylogeny of the fisante clade; a stable classification system for tis component taxa; and hypotheses vis-a-vis eco-biogeographical processes that promoted their speciation and cladogenesis. We shift Francolinus spp. sensu stricto (members of the Spotted Group) and the Unplaced Francolinus gularis from the fisante clade to the patryse [discussed in Mandiwana-Neudani et al., in review]. An Unplaced fisant, F. nahani, is linked with Ptilopachus petrosus (another African endemic partridge ) within the Odontophoridae (New World Quails ). We recognize 25 species of fisante (hereafter spurfowls), including seven with subspecies. They comprise 34 terminal taxa placed within a single genus, Pternistis, sister to Ammoperdix and Perdicula spp., Coturnix quails and Alectoris partridges , within the now monophyletic Coturnicinae. Only one of four putative Groups of spurfowls, the Bare-throated Group, is monophyletic. The other three Groups (Montane, Scaly and Vermiculated) are para- or polyphyletic. Several species pairs of spurfowls, most notably P. afer and cranchii, hybridize in para/sympatry. One Bare-throated spurfowl, P. rufopictus, may be the product of stabilized hybridization between P. afer and/or cranchii and P. leucoscepus.

evolutionary biology