Birds, molecules, and evolutionary patterns among Africa's islands in the sky

Includes bibliographical references.Combing results from phylogenetic and population level studies suggests that climatic cycling has had a profound influence on montane bird speciation in Africa. The results from this thesis suggest that there is deep genetic divergence between many clades (8-12%) of montane passerine birds in Africa, with some shallow divergence towards the tips (4-6%). For widespread species reciprocal monophyly has not been reached in some instances, but generally there is some support for the refuge idea that isolation (fragmentation) of montane forests has facilitated speciation. However, most speciation events happened well before the Pleistocene and therefore the Pleistocene Refugia Hypothesis is not appropriate as a model with which to explain patterns of montane bird diversification in Africa. Rather, both dispersal and vicariance have played important roles in shaping montane bird communities. Thus, a refugia type model does work, but only within the context of pulsed or cyclic expansion and contraction of montane forests, supported in thus study by the consistent recovery of spatially structured areas of endemism, despite varying temporal dynamics

Resource use by two morphologically similar insectivorous bats (Nycteris thebaica and Hipposideros caffer)

Studies of morphologically dissimilar insectivorous bats have lead to the conclusion that morphology is the prime correlate of habitat use, and consequently of diet. This has lead to the prediction that morphologically similar bats should have similar diets. We examined the diet and morphology of two morphologically similar species, the slit-faced bat, Nycteris thebaica, and Sundevall's leaf-nosed bat, Hipposideros caffer, in the context of this prediction. Although both species foraged in the same habitat, they had distinctly different diets. The diet of N. thebaica consisted mainly of non-volant prey, primarily orthopterans and arachnids, and the diet of H. caffer, mainly of moths. Differences in wing design between the two taxa were small. The only significant difference was in aspect ratio. There were no differences in wing loading and wingtip shape ratio between the two species. The flying abilities reported for these two species are very similar, suggesting that these small differences in wing design do not translate into differences in flying ability, and cannot explain the dietary differences between these two species. On the other hand, there are marked differences in their prey detection systems which correspond to differences in their diets. H. caffer uses echolocation to detect the flapping wings of insect prey, whereas N. thebaica depends on prey-generated sounds (fluttering or scuffling) to locate its targets

Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions

Movement ecology and sex are linked to barn owl microbial community composition.

The behavioural ecology of host species is likely to affect their microbial communities, because host sex, diet, physiology, and movement behaviour could all potentially influence their microbiota. We studied a wild population of barn owls (Tyto alba) and collected data on their microbiota, movement, diet, size, coloration, and reproduction. The composition of bacterial species differed by the sex of the host and female owls had more diverse bacterial communities than their male counterparts. The abundance of two families of bacteria, Actinomycetaceae and Lactobacillaceae, also varied between the sexes, potentially as a result of sex differences in hormones and immunological function, as has previously been found with Lactobacillaceae in the microbiota of mice. Male and female owls did not differ in the prey they brought to the nest, which suggests that dietary differences are unlikely to underlie the differences in their microbiota. The movement behaviour of the owls was associated with the host microbiota in both males and females because owls that moved further from their nest each day had more diverse bacterial communities than owls that stayed closer to their nests. This novel result suggests that the movement ecology of hosts can impact their microbiota, potentially on the basis of their differential encounters with new bacterial species as the hosts move and forage across the landscape. Overall, we found that many aspects of the microbial community are correlated with the behavioural ecology of the host and that data on the microbiota can aid in generating new hypotheses about host behaviour

Hidden Diversity—A New Speciose Gall Midge Genus (Diptera: Cecidomyiidae) Associated with Succulent Aizoaceae in South Africa

Aizoaceae (Caryophyllales) constitute one of the major floral components of the unique Greater Cape Floristic Region (GCFR), with more than 1700 species and 70% endemism. Within succulent Aizoaceae, the subfamily Ruschioideae is the most speciose and rapidly diversifying clade, offering potential niches for the diversification of specialized herbivorous insects. Nevertheless, insect diversity on these plants has not been studied to date, and knowledge of gall-inducing insects in the Afrotropics is generally scarce. Our recent observations indicate that succulent Aizoaceae in the GCFR support a rich and largely unstudied community of gall midges (Diptera: Cecidomyiidae). Here, we provide a first report of their diversity with a description of a new genus, Ruschiola Dorchin, and ten new species, based on morphological and molecular analyses of material collected during a three-year targeted survey across major GCFR vegetation types. A high degree of morphological uniformity in Ruschiola suggests recent diversification and necessitated the use of molecular data and laboratory rearing from host plants to verify species boundaries and host ranges

Genetic variation among western populations of the Horned Lark (Eremophila alpestris) indicates recent colonization of the Channel Islands off southern California, mainland-bound dispersal, and postglacial range shifts

© 2014 American Ornithologists\u27 Union. The Channel Islands off the coast of southern California host \u3e50 species of terrestrial vertebrates with varying degrees of phenotypic differentiation. However, most organisms that breed on the Channel Islands remain unstudied with respect to genetic differentiation from mainland populations. By comparing patterns of genetic variation between the Channel Islands and the mainland, we aimed to further our understanding of the role that the Channel Islands have played in diversification of the North American biota. We evaluated long-standing, untested hypotheses regarding colonization patterns and evolutionary relationships among western populations of the Horned Lark (Eremophila alpestris), including the endemic Channel Island subspecies E. a. insularis. We also examined how many times Horned Larks have colonized the Channel Islands, whether the species exhibits asymmetrical patterns of gene flow between mainland and island populations, and whether E. a. strigata of the Pacific Northwest is closely related to the phenotypically similar, but geographically separated, island subspecies. We found that E. a. insularis is polyphyletic, which suggests either multiple colonization events from the mainland or incomplete lineage sorting of a large ancestral population. We also inferred higher rates of migration from the Channel Islands to the mainland, with E. a. strigata being closely related to individuals from the Channel Islands and coastal southern California. Moreover, ecological niche models for E. a. strigata identified suitable abiotic conditions in southern California and the Pacific Northwest during the Last Glacial Maximum, which suggests that E. a. strigata experienced a postglacial range shift in addition to a population bottleneck. Our results provide novel insight regarding the origins of the Channel Island avifauna and the evolutionary history of the Horned Lark in the western United States. Moreover, our findings suggest that Channel Island birds may be weakly differentiated from mainland populations despite phenotypic differences between recognized subspecies

Insights and approaches using deep learning to classify wildlife.

The implementation of intelligent software to identify and classify objects and individuals in visual fields is a technology of growing importance to operatives in many fields, including wildlife conservation and management. To non-experts, the methods can be abstruse and the results mystifying. Here, in the context of applying cutting edge methods to classify wildlife species from camera-trap data, we shed light on the methods themselves and types of features these methods extract to make efficient identifications and reliable classifications. The current state of the art is to employ convolutional neural networks (CNN) encoded within deep-learning algorithms. We outline these methods and present 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 demonstrate the application of 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 in some cases are 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. We then interpret the features in the image where the strongest responses occur, and present dataset biases that were revealed by these extracted features. 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 the relative unfamiliarity of images that were not part of the training set when these images were one of the 20 species "known" to our CNN in contrast to images of the species that were "unknown" to our CNN

A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for a role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages