Patterns of Diversification in a Neotropical Radiation of Birds (Aves: Furnariidae)

Ecology and the role of natural selection in lineage diversification has been a central topic in evolutionary biology since Darwin. At the macroevolutionary scale, this idea is embodied in the ecological theory of adaptive radiation, which posits that rapid diversification is driven by ecological adaptive radiation in which speciation is coupled with niche divergence. Within species, the theory of ecological speciation proposes that local adaptation drives speciation by reducing gene flow among populations occupying different environments either by directly reducing migration or by reducing the fitness of migrants. Much progress has been made testing these predictions in a multitude of organisms, but there remains a lack of studies addressing the role of ecology in diversification at multiple evolutionary scales within the same lineage. Herein, I use the Neotropical bird radiation of ovenbirds (Passeriformes: Furnariidae) as a model system to examine the role of ecology in speciation and lineage diversification. I show that, across furnariid subclades, rates of lineage diversification are best predicted by the rate of climatic-niche evolution rather than ecomorphological evolution, although both are clearly important. This result is consistent with a role for environmental gradients in driving speciation through the process of isolation-by-adaptation (IBA). I then compared the relative support for IBA against the null model of isolation-by-distance (IBD) in a species of furnariid, Cranioleuca antisiensis, that shows signs of incipient speciation and is distributed across a broad environmental gradient. Using genetic, phenotypic, and environmental data from across its distribution, I found evidence of local adaptation in body size. However, I found that IBD was the best explanation for genetic differentiation along the cline, suggesting a limited role for the environmental gradient in reducing gene flow among populations of C. antisiensis. Finally, I explore the properties of the speciation mechanism ‘speciation-by-extinction’. Speciation-by-extinction (SBE) is an alternative to the standard model of allopatric speciation where speciation results from divergence accrued following the isolation of two undifferentiated populations. SBE, in contrast, proposes that speciation can result from the partitioning of standing phenotypic or genetic variation through the local extinction of intermediate populations

Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae)

© 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution. Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic-niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic-niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic-niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic-niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined

Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds

Background Bird plumage exhibits a diversity of colors that serve functional roles ranging from signaling to camouflage and thermoregulation. However, birds must maintain a balance between evolving colorful signals to attract mates, minimizing conspicuousness to predators, and optimizing adaptation to climate conditions. Examining plumage color macroevolution provides a framework for understanding this dynamic interplay over phylogenetic scales. Plumage evolution due to a single overarching process, such as selection, may generate the same macroevolutionary pattern of color variation across all body regions. In contrast, independent processes may partition plumage and produce region-specific patterns. To test these alternative scenarios, we collected color data from museum specimens of an ornate clade of birds, the Australasian lorikeets, using visible-light and UV-light photography, and comparative methods. We predicted that the diversification of homologous feather regions, i.e., patches, known to be involved in sexual signaling (e.g., face) would be less constrained than patches on the back and wings, where new color states may come at the cost of crypsis. Because environmental adaptation may drive evolution towards or away from color states, we tested whether climate more strongly covaried with plumage regions under greater or weaker macroevolutionary constraint. Results We found that alternative macroevolutionary models and varying rates best describe color evolution, a pattern consistent with our prediction that different plumage regions evolved in response to independent processes. Modeling plumage regions independently, in functional groups, and all together showed that patches with similar macroevolutionary models clustered together into distinct regions (e.g., head, wing, belly), which suggests that plumage does not evolve as a single trait in this group. Wing patches, which were conserved on a macroevolutionary scale, covaried with climate more strongly than plumage regions (e.g., head), which diversified in a burst. Conclusions Overall, our results support the hypothesis that the extraordinary color diversity in the lorikeets was generated by a mosaic of evolutionary processes acting on plumage region subsets. Partitioning of plumage regions in different parts of the body provides a mechanism that allows birds to evolve bright colors for signaling and remain hidden from predators or adapt to local climatic conditions

Erratum: Correction: A latitudinal phylogeographic diversity gradient in birds (PLoS biology (2017) 15 4 (e2001073))

[This corrects the article DOI: 10.1371/journal.pbio.2001073.]

Positive association between population genetic differentiation and speciation rates in New World birds

An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from173 NewWorld bird species (\u3e17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted impacts of divergence, gene flow and selection across organisms, but comparisons are complicated by biases introduced during dataset assembly. Sequence similarity thresholds allow the de novo assembly of short reads into clusters of alleles representing different loci, but the resulting datasets are sensitive to both the similarity threshold used and to the variation naturally present in the organism under study. Thresholds that require high sequence similarity among reads for assembly (stringent thresholds) as well as highly variable species may result in datasets in which divergent alleles are lost or divided into separate loci (‘over-splitting’), whereas liberal thresholds increase the risk of paralogous loci being combined into a single locus (‘under-splitting’). Comparisons among datasets or species are therefore potentially biased if different similarity thresholds are applied or if the species differ in levels of within-lineage genetic variation. We examine the impact of a range of similarity thresholds on assembly of empirical short read datasets from populations of four different non-model bird lineages (species or species pairs) with different levels of genetic divergence. We find that, in all species, stringent similarity thresholds result in fewer alleles per locus than more liberal thresholds, which appears to be the result of high levels of over-splitting. The frequency of putative under-splitting, conversely, is low at all thresholds. Inferred genetic distances between individuals, gene tree depths, and estimates of the ancestral mutation-scaled effective population size (θ) differ depending upon the similarity threshold applied. Relative differences in inferences across species differ even when the same threshold is applied, but may be dramatically different when datasets assembled under different thresholds are compared. These differences not only complicate comparisons across species, but also preclude the application of standard mutation rates for parameter calibration. We suggest some best practices for assembling short read data to maximize comparability, such as using more liberal thresholds and examining the impact of different thresholds on each dataset

Aves del Parque Nacional Natural Chingaza y zona de amortiguación, Cordillera Oriental de Colombia

We describe the bird species composition in the Chingaza National Park and its buffer zone, based on a revision of 10 published studies, recent fieldwork between 2008-2017, and the Colombia Bio expedition on 2018. We report 531 species for the Chingaza National Park and its buffer zone, grouped in 339 genera and 57 families. Six species are endemic to Colombia, 14 are near-endemic, 1 is critically endangered, 6 are endangered, 4 are vulnerable, 3 are near-threatened and 37 are migratory. This list includes 149 species more than those comprised in previous information from published datasets and ornithological collections. Additionally, we generated genetic barcodes, based sequences of the mtDNA gene COI, for 74 species, and present the first genetic record from Colombia in Barcode of Life Datasystems (BOLD) for Dysithamnus leucostictus, Chamaeza turdina, Rupicola peruvianus, Atlapetes semirufus, Euphonia mesochrysa and Chlorospingus flavopectus olsoni. This list is a tool to promote the study and conservation of birds in this area of the Colombian Eastern Cordillera.Describimos la composición de especies de aves del Parque Nacional Natural (PNN) Chingaza y su zona de amortiguación, a partir de la revisión de 10 estudios ornitológicos, trabajo de campo entre 2008–2017 y la expedición Colombia Bio en 2018. Reportamos para el PNN Chingaza y su zona de amortiguación un total de 531 especies, agrupadas en 339 géneros y 57 familias. Seis especies presentes en el parque son endémicas de Colombia, 14 casi endémicas, 1 en peligro crítico, 6 en peligro, 4 vulnerables, 3 casi amenazadas y 37 migratorias. Esta lista incluye 149 especies adicionales a la información previamente conocida por datos publicados y colecciones ornitológicas. Adicionalmente, generamos códigos de barras genéticos, con base en secuencias del gen mitocondrial COI, para 74 especies y presentamos los primeros registros genéticos de Colombia en la plataforma para códigos de barra genéticos Barcode of Life Datasystems (BOLD) para Dysithamnus leucostictus, Chamaeza turdina, Rupicola peruvianus, Atlapetes semirufus, Euphonia mesochrysa y Chlorospingus flavopectus olsoni.  El presente listado es una herramienta para incentivar el estudio y conservación de las aves en este sector de la Cordillera Oriental colombiana

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong