33 Works

Data from: Evidence for ephemeral ring species formation during the diversification history of Western Fence Lizards (Sceloporus occidentalis)

Nassima Bouzid, James Archie, Roger Anderson, Jared Grummer & Adam Leaché
Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographic structure and evolutionary history of population divergence within Sceloporus occidentalis (Western Fence Lizards), a habitat generalist with a broad distribution that spans the major biogeographic regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny, and demography. Population...

Data from: De novo transcriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set

Sonal Singhal
High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without a high-quality reference genome. For every stage of analysis – from assembly to annotation to variant discovery – researchers have to distinguish technical artefacts from the biological realities of their data before...

Data from: Trait evolution, resource specialization and vulnerability to plant extinctions among Antillean hummingbirds

Bo Dalsgaard, Jonathan D. Kennedy, Benno I. Simmons, Andrea C. Baquero, Ana M. Martín González, Allan Timmermann, Pietro K. Maruyama, Jimmy A. McGuire, Jeff Ollerton, William J. Sutherland & Carsten Rahbek
Species traits are thought to predict feeding specialisation and the vulnerability of a species to extinctions of interaction partners, but the context in which a species evolved and currently inhabits may also matter. Notably, the predictive power of traits may require that traits evolved to fit interaction partners. Furthermore, local abiotic and biotic conditions may be important. On islands, for instance, specialised and vulnerable species are predicted to be found mainly in mountains, whereas species...

Data from: Microgeographic socio-genetic structure of an African cooperative breeding passerine revealed: integrating behavioural and genetic data.

Ângela M Ribeiro, Penn Lloyd, Kevin A Feldheim & Rauri C K Bowie
Dispersal can be motivated by multiple factors including sociality. Dispersal behaviour affects population genetic structure that in turn reinforces social organization. We combined observational information with individual-based genetic data in the Karoo scrub-robin, a facultative cooperatively breeding bird, to understand how social bonds within familial groups affect mating patterns, cause sex asymmetry in dispersal behavior and ultimately influence the evolution of dispersal. Our results revealed that males and females do not have symmetrical roles in...

Data from: Museum genomics: low-cost and high-accuracy genetic data from historical specimens

Kevin C. Rowe, Sonal Singhal, Matthew D. MacManes, Julien F. Ayroles, Toni Lyn Morelli, Emily M. Rubidge, Ke Bi & Craig C. Moritz
Natural history collections are unparalleled repositories of geographic and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical...

Data from: Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs

Rayna C Bell, Jason B MacKenzie, Michael J Hickerson, Krystle L Chavarría, Michael Cunningham, Stephen Williams, Craig Moritz, K. L. Chavarria, J. B. MacKenzie, S. Williams, R. C. Bell, M. Cunningham, C. Moritz & M. J. Hickerson
Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum (LGM). Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species’ responses to...

Data from: Microgeographic socio-genetic structure of an African cooperative breeding passerine revealed: integrating behavioural and genetic data.

Ângela M Ribeiro, Penn Lloyd, Kevin A Feldheim & Rauri C K Bowie
Dispersal can be motivated by multiple factors including sociality. Dispersal behaviour affects population genetic structure that in turn reinforces social organization. We combined observational information with individual-based genetic data in the Karoo scrub-robin, a facultative cooperatively breeding bird, to understand how social bonds within familial groups affect mating patterns, cause sex asymmetry in dispersal behavior and ultimately influence the evolution of dispersal. Our results revealed that males and females do not have symmetrical roles in...

Data from: A tight balance between natural selection and gene flow in a southern African arid-zone endemic bird

Ângela Maria Ribeiro, Penn Lloyd & Rauri C. K. Bowie
Gene flow is traditionally thought to be antagonistic to population differentiation and local adaptation. However, recent studies have demonstrated that local adaptation can proceed provided that selection is greater than the homogenising effects of gene flow. We extend these initial studies by combining ecology (climate), phenotype (body size), physiological genetics (oxidative phosphorylation genes) and neutral loci (nuclear microsatellites and introns) to test whether selection can counter-balance gene flow and hence promote local adaptation in a...

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