Bioacoustics in cognitive research: Applications, considerations, and recommendations.

The multifaceted ability to produce, transmit, receive, and respond to acoustic signals is widespread in animals and forms the basis of the interdisciplinary science of bioacoustics. Bioacoustics research methods, including sound recording and playback experiments, are applicable in cognitive research that centers around the processing of information from the acoustic environment. We provide an overview of bioacoustics techniques in the context of cognitive studies and make the case for the importance of bioacoustics in the study of cognition by outlining some of the major cognitive processes in which acoustic signals are involved. We also describe key considerations associated with the recording of sound and its use in cognitive applications. Based on these considerations, we provide a set of recommendations for best practices in the recording and use of acoustic signals in cognitive studies. Our aim is to demonstrate that acoustic recordings and stimuli are valuable tools for cognitive researchers when used appropriately. In doing so, we hope to stimulate opportunities for innovative cognitive research that incorporates robust recording protocols. This article is categorized under: Neuroscience > Cognition Psychology > Theory and Methods Neuroscience > Behavior Neuroscience > Cognition.

Phylogeography of the Rufous Vanga and the role of bioclimatic transition zones in promoting speciation within Madagascar.

Madagascar is known as a biodiversity hotspot, providing an ideal natural laboratory for investigating the processes of avian diversification. Yet, the phylogeography of Madagascar's avifauna is still largely unexamined. In this study, we evaluated phylogeographic patterns and species limits within the Rufous Vanga, Schetba rufa, a monotypic genus of forest-dwelling birds endemic to the island. Using an integrative taxonomic approach, we synthesized data from over 4000 ultra-conserved element (UCE) loci, mitochondrial DNA, multivariate morphometrics, and ecological niche modeling to uncover two reciprocally monophyletic, geographically circumscribed, and morphologically distinct clades of Schetba. The two lineages are restricted to eastern and western Madagascar, respectively, with distributions broadly consistent with previously described subspecies. Based on their genetic and morphological distinctiveness, the two subspecies merit recognition as separate species. The bioclimatic transition between the humid east and dry west of Madagascar likely promoted population subdivision and drove speciation in Schetba during the Pleistocene. Our study is the first evidence that an East-West bioclimatic transition zone played a role in the speciation of birds within Madagascar.

Hidden diversity of forest birds in Madagascar revealed using integrative taxonomy.

Madagascar is renowned as a global biodiversity hotspot with high levels of microendemism. However, there are few molecular phylogenetic studies of Malagasy birds, particularly for forest-dwelling species, signifying a substantial gap in current measures of species diversity in the absence of genetic data. We evaluated species limits and explored patterns of diversification within the genus Newtonia (Family Vangidae), a group of forest-dwelling songbirds endemic to Madagascar. Our modern systematics approach combined genomic, morphometric, and ecological niche data to analyze the evolutionary history of the group. Our integrative analysis uncovered hidden species-level diversity within N. amphichroa, with two deeply divergent and morphologically distinct lineages isolated in different regions of humid forest. We describe the southern lineage as a new species. Conversely, N. brunneicauda, which we initially hypothesized may harbor cryptic diversity owing to its large distribution spanning a range of habitats, was found to have no distinct lineages and shared haplotypes across much of its distribution. The contrasting diversification patterns between Newtonia lineages may be the result of their elevational tolerances. Newtonia brunneicauda has a broad habitat tolerance and elevational range that appears to have facilitated population expansion and gene flow across the island, limiting opportunities for diversification. On the other hand, N. amphichroa is found predominantly in mid-elevation and montane humid forests, a restriction that appears to have promoted speciation associated with climatic fluctuations during the Pleistocene. Our findings indicate that species diversity of Malagasy forest-dwelling birds may be greater than currently recognized, suggesting an urgent need for further studies to quantify biodiversity in Madagascar's rapidly disappearing native forests.

Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens).

The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.

Untangling taxonomic confusion and diversification patterns of the Streak-breasted Scimitar Babblers (Timaliidae: Pomatorhinus ruficollis complex) in southern Asia.

Biodiversity patterns in Asia are poorly understood due to inferences drawn from incorrect taxonomy and limited survey effort. The Streak-breasted Scimitar Babblers (Pomatorhinus ruficollis complex) have a wide distribution across southern Asia and exhibit a high degree of plumage variability within and among populations. Continued use of traditional subspecies designations over revised species-limits based on plumage and DNA sequence data furthers confusion in this group and obscures complex biogeographic patterns. In this study, we combined previously published DNA sequences with newly sampled populations to produce a comprehensive dataset for the ruficollis complex. Phylogenetic analysis of these data confirms that traditional subspecies based on plumage alone are paraphyletic and therefore not good descriptors of evolutionary history. With increased sampling, our study supported previous delimitations of phylogenetic species as distinct units, refined the range limits of two taxa - P. reconditus (throughout central China) and P. nigrostellatus (Hainan, Guangxi, N Vietnam), showed two additional clades that may be distinct species, and uncovered a 'suture' zone where populations of multiple species occur in the same localities. Diversification within the ruficollis complex indicates a clade of Sino-Himalayan and SE Asian species sister to a clade distributed in central and southern China species. The 'suture' zone where different ruficollis species are in contact coincides with the meeting of these four major geographic areas in a highly geomorphologically complex region.

Taxonomic consequences of cryptic speciation in the Golden Whistler Pachycephala pectoralis complex in mainland southern Australia.

The Golden Whistler (Aves: Passeriformes: Pachycephalidae) Pachycephala pectoralis sensu lato has long played a key role in the development of the theory of allopatric speciation (Mayr 1932a, b; Mayr 1942; Galbraith 1956). The P. pectoralis species complex formerly comprised 60-70 nominal subspecies and so had a distribution spanning the Indo-Pacific (Boles 2007). More recent taxonomic treatments consider the complex as multiple species-level taxa largely circumscribed by geography (Dickinson and Christidis 2014; Gill and Donsker 2014). In Australia, the endemic species P. pectoralis sensu stricto is sympatric with the closely related Mangrove Golden Whistler P. melanura. However, as the latter's English name suggests, P. melanura is closely tied to mangroves in Australia, southeast New Guinea, and islets in the Bismarck Archipelago. Diagnostic plumage traits separating the two species are subtle: males of P. melanura have more extensively black tails and a greyer upper surface to the remiges, and females are usually yellower ventrally. All Pachycephala species, especially those in the P. pectoralis-melanura species complex, have recently become the focus of DNA sequence-based studies (Jønsson et al. 2008, 2014; Andersen et al. 2014). Data from most populations have now been analysed phylogenetically to better understand relationships and thus the history of evolution and speciation processes within and between both species. This has also been used in studies of the group's historical biogeography to provide information as to the age of taxa and their spread across oceanic archipelagos and continents (Jønsson et al. 2014). Here we discuss the taxonomic implications of a result that has emerged consistently and independently in these studies, concerning the systematics of the southern Australian populations in south-eastern and south-western Australia, both of which have been ascribed to P. p. fuliginosa since Galbraith (1956), and we show that the name P. occidentalis Ramsay, 1878 is available for the western population and should be used for it. 

Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus).

We present the first extensive and integrative analysis of niche evolution based on climatic variables and a dated molecular phylogeny of a heterogeneous avian group of Southeast Asian scimitar babblers of the genus Pomatorhinus. The four main clades of scimitar babblers have species that co-occur in similar areas across southern Asia but some have diverged at different timeframes, with the most recently evolved clade harboring the highest number of species. Ecological niche models and analysis of contributing variables within a phylogenetic framework indicate instances of convergent evolution of members of different clades onto similar ecological parameter space, as well as divergent evolution of members from within clades. Pomatorhinus species from different clades occupying Himalayan foothills show convergence towards similar climatic tolerances, whereas within a clade, allopatric sister-species occurring in the Himalayas have diverged to occupy different climatic parameter spaces. Comparisons of climatic tolerances of Himalayan foothills taxa with species distributed further south in Assam/Burma and Burma/Thailand indicate convergence towards similar parameter spaces in several climatic variables. Niche overlap was observed to be lower among species of the youngest clade (ruficollis) and higher among species of older clades (ferruginosus). Analysis of accumulation of ecological disparity through time indicates rapid divergence within recent time frames. As a result, Himalayan taxa originating at different temporal scales within the four main scimitar babbler clades have differentiated ecologically only in recently diverged taxa. Our study suggests that the repeated orogenic and climatic fluctuations of the Pliocene and Pleistocene within mainland Southeast Asia served as an important ecological speciation driver within scimitar babblers, by providing opportunities for rapid geographic expansion and filling of novel environmental niches.

SandflyMap: leveraging spatial data on sand fly vector distribution for disease risk assessments.

We feature SandflyMap (www.sandflymap.org), a new map service within VectorMap (www.vectormap.org) that allows free public online access to global sand fly, tick and mosquito collection records and habitat suitability models. Given the short home range of sand flies, combining remote sensing and collection point data give a powerful insight into the environmental determinants of sand fly distribution. SandflyMap is aimed at medical entomologists, vector disease control workers, public health officials and health planners. Data are checked for geographical and taxonomic errors, and are comprised of vouchered specimen information, and both published and unpublished observation data. SandflyMap uses Microsoft Silverlight and ESRI's ArcGIS Server 10 software platform to present disease vector data and relevant remote sensing layers in an online geographical information system format. Users can view the locations of past vector collections and the results of models that predict the geographic extent of individual species. Collection records are searchable and downloadable, and Excel collection forms with drop down lists, and Excel charts to country, are available for data contributors to map and quality control their data. SandflyMap makes accessible, and adds value to, the results of past sand fly collecting efforts. We detail the workflow for entering occurrence data from the literature to SandflyMap, using an example for sand flies from South America. We discuss the utility of SandflyMap as a focal point to increase collaboration and to explore the nexus between geography and vector-borne disease transmission.

Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae).

The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster.

The differential effect of lowlands on the phylogeographic pattern of a Mesoamerican montane species (Lepidocolaptes affinis, Aves: Furnariidae).

We sequenced 1869 bp of mtDNA (cyt b and ND2) from 80 specimens of Lepidocolaptes affinis, a montane bird species of Mesoamerica, sampled at 34 localities from Mexico to Costa Rica. The species showed moderate genetic diversity (π=0.0045) and phylogeographic structure (Φ(ST)=0.12-0.95). The phylogeographic pattern indicated the Nicaragua Depression has prevented gene flow whereas populations on the two sides of the Isthmus of Tehuantepec did not show strong genetic differentiation. In Mexico, the population of the Sierra Madre Oriental was composed of two different lineages. In general, our data did not support a scenario of historical demographic expansion, and matched partially the phylogeographic patterns of other Mesoamerica montane species.

Phylogenetic relationships of flowerpeckers (Aves: Dicaeidae): novel insights into the evolution of a tropical passerine clade.

Understanding the relationships and evolution of flowerpeckers has been challenging, particularly as no phylogenetic study has as yet assessed the group. Here, we present a first such analysis of this clade based on sequences of two mitochondrial genes and one nuclear intron. Our analyses offer strong support for monophyly of the Dicaeidae. Within the family, 4 Dicaeum species (D. chrysorrheum, D. melanoxanthum, D. agile, and D. everetii) had closer affinity to Prionochilus, although tests of alternative topologies could not reject reciprocal monophyly of the two genera. Across the family, overall bill shape trends from more stout bills basally to more slender and medium bills, whereas sexual dichromatism and plumage patterns show much more homoplasy. Taxonomically, generic allocations may need to be changed to reflect historical relationships better.

Ecological niche conservatism and Pleistocene refugia in the Thrush-like Mourner, Schiffornis sp., in the neotropics.

Recent studies have increasingly implicated deep (pre-Pleistocene) events as key in the vertebrate speciation, downplaying the importance of more recent (Pleistocene) climatic shifts. This work, however, has been based almost exclusively on evidence from molecular clock inferences of splitting dates. We present an independent perspective on this question, using ecological niche model reconstructions of Pleistocene Last Glacial Maximum (LGM) potential distributions for the Thrush-like Mourner (Schiffornis turdina) complex in the neotropics. LGM distributional patterns reconstructed from the niche models relate significantly to phylogroups identified in previous molecular systematic analyses. As such, patterns of differentiation and speciation in this complex are consistent with Pleistocene climate and geography, although further testing will be necessary to establish dates of origin firmly and unambiguously.

Locating pleistocene refugia: comparing phylogeographic and ecological niche model predictions.

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution.

Phylogeographic patterns, molecular and vocal differentiation, and species limits in Schiffornis turdina (Aves).

Establishing species limits can be challenging for organisms in which few variable morphological characters are available, such as Schiffornis turdina, a Neotropical suboscine bird of long-debated taxonomic affinities. Apart from its dull plumage and secretive behavior, this taxon is well-known for its subtle but discrete within-species geographic variation in vocalizations. Phylogeographic reconstruction based on three mitochondrial markers sampled across much of the species' range reveals substantial structuring, concordant with recognized areas of endemism in Neotropical lowland forests. Monophyly of S. turdina was weakly supported by the combined dataset, as was the basal position of the Guyanan Shield population with regard to other S. turdina clades. Based on the results from both genetic and a preliminary, qualitative analysis of vocalizations, I recommend revised species limits to reflect more accurately the evolutionary history of this complex.