John Carpenter

and 5 more

New World wood warblers (family: Parulidae) can exhibit strong phenotypic differences among species, particularly in song and plumage. However, within-species variation in these warblers—often designated as subspecies—is much more subtle and has led to significant debate over the origin, maintenance, and conservation status of populations that differ. A species that exhibits controversial subspecific status is the black-throated green warbler (Setophaga virens), a Neotropical-Nearctic migrant that breeds throughout eastern and boreal North America with several isolated populations at the margins of its range. In particular, uncertainty has lingered over the status of S. v. waynei, a disjunct population along the southeast Atlantic Coastal Plain of the United States that differs morphologically and ecologically from the nominate subspecies. Despite its unique circumstances, the subspecific status of S. v. waynei remains questionable in the absence of any population-wide genomic analyses. Here, we employ whole-genome resequencing to estimate the genetic distinctiveness among samples collected across the entirety of S. virens breeding range, including from putative S. v. waynei. Despite detecting low global differentiation (FST = 0.027) across the entire species, we observed discrete genetic clustering among S. v. waynei. Principal components analysis of genome-wide differences shows the main axis of variation separates S. v. waynei from all other S. v. virens samples. We also found that S. v. waynei is most similar to another isolated population from the Piedmont of North Carolina and detected evidence of a historical north-to-south geographic dispersal among the entire complex. Combined with previously documented ecological and morphological distinctness, our results support that S. v. waynei be considered a distinct and recognized subspecies worthy of targeted conservation efforts.

Caitlin Miller

and 13 more

Identifying genetic conservation units (CUs) in threatened species is critical for the preservation of adaptive capacity and evolutionary potential in the face of climate change. However, delineating CUs in highly mobile species remains a challenge due to high rates of gene flow and genetic signatures of isolation by distance. Even when CUs are delineated in highly mobile species, the CUs often lack key biological information about what populations have the most conservation need to guide management decisions. Here we implement a framework for rigorous CU identification in the Canada Warbler (Cardellina canadensis), a highly mobile migratory bird species of conservation concern, and then integrate demographic modeling and genomic offset within a CU framework to guide conservation decisions. We find that whole-genome structure in this highly mobile species is primarily driven by putative adaptive variation. Identification of CUs across the breeding range revealed that Canada Warblers fall into two Evolutionarily Significant Units (ESU), and three putative Adaptive Units (AUs) in the South, East and Northwest. Quantification of genomic offset within each AU reveals significant spatial variation in climate vulnerability, with the Northwestern AU being identified as the most vulnerable to future climate change based on genomic offset predictions. Alternatively, quantification of past population trends within each AU revealed the steepest population declines have occurred within the Eastern AU. Overall, we illustrate that genomics-informed CUs provide a strong foundation for identifying current and potential future regional threats that can be used to manage highly mobile species in a rapidly changing world.

Aubrie James

and 2 more

An underdeveloped but potentially valuable molecular method in ecology is the ability to quantify the frequency with which foraging pollinators carry different plant pollens. Thus far, DNA metabarcoding has only reliably identified the presence/absence of a plant species in a pollen sample, but not its relative abundance in a mixed sample. Here we use a system of four congeneric, co-flowering plants in the genus Clarkia and their bee pollinators to (1) develop a molecular method to quantify different Clarkia pollens found on foraging bees; and (2) determine if bee pollinators carry Clarkia pollens in predictable ways, based on knowledge of their foraging behaviors. We develop a molecular method we call quantitative amplicon sequencing (qAMPseq) which varies cycling number (20, 25, 30, and 35 cycles) in polymerase chain reaction (PCR), individually indexing the same samples in different cycle treatments, and sequencing the resulting amplicons. These values are used to approximate an amplification curve for each Clarkia species in each sample, similar to the approach of quantitative PCR, which can then be used to estimate the relative abundance of the different Clarkia species in the sample. Using this method, we determine that bee visitation behaviors are generally predictive of the pollens that bees carry while foraging. We also show that some bees carry multiple species of Clarkia at the same time, indicating that Clarkia likely compete via interspecific pollen transfer. In addition to adding a ‘missing link’ between bee visitation behavior and actual pollen transfer, we suggest qAMPseq as another molecular method to add to the developing molecular ecology and pollination biology toolbox.