Jason T. Weir's research while affiliated with Royal Ontario Museum and other places

... That is, for a fuller assessment of the history of a taxonomic group, nuclear genes that mutate at different rates must be included. In addition, new methods have allowed for genome scanning and these have proven very useful in the discovery of mito-nuclear discordance, and even speciation in the presence of gene flow with introgression (see e.g., Kunerth et al., 2022;Mikkelsen & Weir, 2023;Perea et al., 2016;Wright et al., 2022). ...

... Average residuals from the regression line of genetic versus geographic distance and 95% confidence intervals from the overall regression line in the studied spider families. In their recent article, Anderson and Weir (2022) showed that, at least in vertebrates, the divergent ecological adaptation is not a common consequence of allopatric speciation; in most of the studied groups, adaptive divergence did not significantly increase in geographically isolated, closely related species. So far, the pattern is less clear for invertebrate animals, especially arthropods. ...

... Connecting across time-scales requires integration of different data types and approaches. Combining genomic, phenotypic and fitness data may allow us to make inferences about the origins of isolation in the present Anderson, López-Fernández and Weir 2023), and also about the temporal stability of these reproductive barriers in the face of gene flow (Kulmuni et al. 2020;Xiong and Mallet 2022). In particular, it is possible to test whether extrinsic (i.e., environment-dependent isolation) is less stable than intrinsic isolation over time, as climates and environments change and allow previously extrinsically isolated lineages to form fertile hybrids and merge back together (Anderson, López-Fernández and Weir 2023). ...

... Unlike magma, during a volcanic eruption, there are no gases released in lava. Disasters caused by volcanic activity (Figure 9) can not only affect the structure of populations over tens of thousands of years, but maintain negative consequences in the long term (Bemmels et al., 2022). ...

... Many lowland terra-firme (non-flooded forest) Amazonian birds have geographically isolated populations across rivers yet experience high levels of gene flow (Barrera-Guzmán et al. 2022;Del-Rio et al. 2022;Musher et al. 2022). Rivers are key biogeographic barriers for many lowland Amazonian birds, driving population isolation and genetic structure across the landscape (Sick 1967;Capparella 1991;Ribas et al. 2012;Smith et al. 2014;Ferreira et al. 2017). ...

... Some of the stream reaches with the highest recorded local abundances of Grass Pickerel are agricultural drains that mirror the shallow slopes, vegetated channels with ample floodplain habitat, and highconductivity (i.e., clay-rich) substrate characteristics of naturally occurring wetland and stream Grass Pickerel habitat [9]. Its Canadian range consists of four disjunct populations that likely originated from a single Pleistocene refugium, but are now geographically and genetically distinct, with contemporary gene flow between populations unlikely [50,51]. Further, a recent analysis of Niagara Peninsula (Ontario) subpopulations suggests that even geographically close subpopulations (< 30 river km) have limited gene flow, perhaps due to habitat barriers to functional movement [50]. ...

... We downloaded raw Illumina sequencing reads and genome assemblies from each of the four available kiwi species from Genbank: great spotted kiwi, little spotted kiwi, Okarito brown kiwi, and North Island brown kiwi [2,14]. We downloaded the raw reads for a southern brown kiwi from the individual with the highest number of available reads [15]. To act as an outgroup for the phylogenomic analyses, we downloaded raw sequencing reads and the genome assembly of emu (Dromaius novaehollandiae) [14]. ...

... Among other causes, this can be a consequence of speciation in sympatry or without clear geographical barriers (Barluenga et al., 2006;Lamichhaney et al., 2017;Martin et al., 2013;Rodríguez-Cajarville et al., 2022;Turbek et al., 2021) or the fact that barriers are more permeable than previously considered (Lavinia et al., 2019;Rodríguez-Gómez et al., 2013;Smith et al., 2014). In this context, the study of diversification and speciation in the Neotropics should not only assess the factors involved but also analyse how diversification occurred, if there is evidence of gene flow and, if this is the case, whether it occurred during diversification or as a consequence of secondary contact (Luzuriaga-Aveiga et al., 2021). ...

... argentatus smithsonianus;Sternkopf et al. 2010), as well as the Willow Flycatcher (Empidonax traillii) and Alder Flycatcher (E. alnorum;Bemmels et al. 2021). ...

... What remains to be determined is whether local species coexistence arose due to trait divergence resulting from resource competition after secondary contact had been established, or from species-sorting that occurred during secondary contact. Trait divergence induced by resource competition after secondary contact can play a significant role in the evolution of diversity in adaptive as well as in non-adaptive radiations (Anderson and Weir 2021;Grant and Grant 2006;Lambert et al. 2019). ...