S. Burgess - Academia.edu (original) (raw)

Papers by S. Burgess

Journal of Biogeography, 2019

Secondary contact between long isolated populations has several possible outcomes. These include ... more Secondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant ("lineage fusion" herein). The latter scenario has rarely been explicitly considered in single-species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next-generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present-day panmictic population is the product of lineage fusion, using an exemplar statistical framework-approximate Bayesian computation. We found that with approximately 100 phased haplotype loci (each 400 bp long) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available. Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long-term population history.

Food Webs, 2019

Food webs based on dead organic matter have received relatively little research attention. Here w... more Food webs based on dead organic matter have received relatively little research attention. Here we focus on dead-wood-dependent (saproxylic) arthropod communities—an overlooked component of forest biodiversity that contributes to decomposition of fallen trees and nutrient cycling. First, we summarized information on factors that impact saproxylic arthropod biodiversity via a descriptive mini-review of the literature, given that the structure of food webs should be contingent upon local community composition, species richness, and/or species abundances within and among neighboring rotting logs. Next, we coupled intensive fieldwork with molecular approaches to taxonomic identification of saproxylic arthropods sampled from rotting logs in the southern Appalachian Mountains, and synthesized information on their feeding ecology, in order to infer trophic interactions. Our descriptive mini-review highlighted major influences of local-scale (site-specific) factors affecting biodiversity, and by extension, food web structure; a pronounced publication bias toward saproxylic beetles from evergreen forests in Europe was also evident. Our empirical data on community composition of rotting logs at intermediate to late stages of decay revealed a complex food web structure. This comprised internal and external primary nutrient sources (dead wood within logs vs. nearby living trees and fallen leaves), a diverse suite of primary consumers (wood-feeding detritivores, leaf litter-feeding detritivores, as well as herbivores and fungivores), several secondary consumer functional groups (omnivorous scavengers and ectoparasites or parasitoids), and top-level carnivorous predators that were mostly made up of spiders, Opiliones, and centipedes. We close by discussing persistent challenges and limitations, and suggest future research directions.

Journal of Biogeography, 2019

Secondary contact between long isolated populations has several possible outcomes. These include ... more Secondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant ("lineage fusion" herein). The latter scenario has rarely been explicitly considered in single-species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next-generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present-day panmictic population is the product of lineage fusion, using an exemplar statistical framework-approximate Bayesian computation. We found that with approximately 100 phased haplotype loci (each 400 bp long) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available. Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long-term population history.

Food Webs, 2019

Food webs based on dead organic matter have received relatively little research attention. Here w... more Food webs based on dead organic matter have received relatively little research attention. Here we focus on dead-wood-dependent (saproxylic) arthropod communities—an overlooked component of forest biodiversity that contributes to decomposition of fallen trees and nutrient cycling. First, we summarized information on factors that impact saproxylic arthropod biodiversity via a descriptive mini-review of the literature, given that the structure of food webs should be contingent upon local community composition, species richness, and/or species abundances within and among neighboring rotting logs. Next, we coupled intensive fieldwork with molecular approaches to taxonomic identification of saproxylic arthropods sampled from rotting logs in the southern Appalachian Mountains, and synthesized information on their feeding ecology, in order to infer trophic interactions. Our descriptive mini-review highlighted major influences of local-scale (site-specific) factors affecting biodiversity, and by extension, food web structure; a pronounced publication bias toward saproxylic beetles from evergreen forests in Europe was also evident. Our empirical data on community composition of rotting logs at intermediate to late stages of decay revealed a complex food web structure. This comprised internal and external primary nutrient sources (dead wood within logs vs. nearby living trees and fallen leaves), a diverse suite of primary consumers (wood-feeding detritivores, leaf litter-feeding detritivores, as well as herbivores and fungivores), several secondary consumer functional groups (omnivorous scavengers and ectoparasites or parasitoids), and top-level carnivorous predators that were mostly made up of spiders, Opiliones, and centipedes. We close by discussing persistent challenges and limitations, and suggest future research directions.