RESEARCH PAPER Genomic evidence of a widespread southern distribution during the Last Glacial Maximum for two eastern North American hickory species

Aim: Phylogeographical studies of temperate forest taxa often infer complex histories involving population subdivision into distinct refugia during the Last Glacial Maximum (LGM). However, some temperate deciduous trees may have been broadly distributed in southeastern North America during the LGM. We investigate genome-wide genetic structure in two widespread eastern North American tree species to determine if range expansion from genetically isolated refugia or from a broader, less genetically subdivided region better explains their post-glacial history. Location: Eastern North America (ENA). Taxa: Bitternut hickory (Carya cordiformis [Wangenh.] K.Koch) and shagbark hickory (Carya ovata [Mill.] K.Koch). Methods: Genetic diversity and differentiation indices were calculated from >1,000 nuclear SNP loci genotyped in ca. 180 individuals per species sampled across ENA. Genetic structure was investigated using principle component analysis and genetic clustering algorithms. As an additional tool for inference, areas of suitable habitat during the LGM were predicted using species distribution models (SDMs). Results: Populations across all latitudes showed similar levels of genetic diversity. Most genetic variation was weakly differentiated across ENA, with the exception of an outlier population of Carya ovata in Texas. Genetic structure in each species exhibited an isolation-by-distance pattern. SDMs predicted high LGM habitat suitability over much of the southeastern United States. Main conclusions: Both hickory species likely survived the LGM in low-density populations that were broadly distributed across southeastern North America and not highly genetically differentiated, except that the range-edge Texas population of Carya ovata may represent a separate glacial refugium. Over most of ENA, genetic structure in both species is best explained by simple latitudinal range shifts and high gene flow among populations, rather than expansions from multiple, genetically isolated refugia as is characteristic of taxa from other Northern Hemisphere temperate regions of the world.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144211/1/Bemmels_et_al-2018-Journal_of_Biogeography.pdf85Description of Bemmels_et_al-2018-Journal_of_Biogeography.pdf : main articl

Species Range Shifts in Dynamic Geological and Climatic Landscapes: Studies in Temperate and Tropical Trees

Spatial patterns in the geographic distributions of ecosystems, species, and genetic variation are the result of both ecological conditions and evolutionary dynamics that have unfolded in a long, historical process. Attempts to account for spatial patterns in biodiversity provided some of the earliest inspiration for the development of the theory of evolution, but more than a century and a half later, biologists are still discovering precisely how and why these patterns arise. As a field, historical biogeography has emphasized the importance of Earth’s geological and climatic history in understanding dynamic spatial biodiversity patterns. It is well known that species and populations respond to geological and climatic change, but the details about how these responses unfolded are often vaguely specified, and the precise ecological mechanisms mediating them are often unknown. My dissertation tests specific hypotheses about historical range shifts and their genetic consequences, using recent advances such as next-generation sequencing, demographic and coalescent modelling, Approximate Bayesian Computation, and large datasets of species occurrence records and species traits. This work spans several arboreal study systems, and aims to provide new insight into unanswered questions and controversial historical biogeographic hypotheses. I begin by considering the effects of glaciation on range shifts in two hickory species from eastern North America. It is not precisely known where most temperate deciduous tree species from this region survived the Last Glacial Maximum, and whether northern populations existed and contributed to postglacial recolonization. I show that both species were likely fairly geographically widespread and genetically connected, and that postglacial recolonization occurred from a northern source in one species and a southern source in another. Next, I develop and test competing hypotheses about the ecological factors mediating postglacial range shifts in canyon live oak from California. I aim to attain mechanistic insight into the drivers of historical range shifts in this geographically complex Mediterranean-climate region, and find that summer drought tolerance was likely a key ecological factor mediating these shifts. Lastly, I zoom out in scale and ask how long-term migrational responses to geological and climatic change affect the assembly of entire communities. I examine the biogeographic distributions of >1,000 Neotropical rainforest woody plant species, and show that traits such as drought tolerance and elevational range have impacted the ability of species to disperse across or around the biogeographic filter created by Pliocene uplift of the northern Andes and formation of dry habitats in northeastern South America. Overall, my dissertation work has revealed the importance of species-specific responses to geological and climatic change, and how these responses affect the geographic distribution of biodiversity (from genetic to species to community levels). I test hypotheses concerning the geographic locations from which range shifts occurred (in hickories), the ecological factors mediating range shifts in complex environments (in canyon live oak), and the community-wide impact of species traits on biogeographic dispersal (in Neotropical trees). This work contributes to a growing body of knowledge helping transform historical biogeography from a realm of broad patterns, into a field where new insight can be gained by accounting for species-specific histories and the ecological processes that mediate range shifts.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/144154/1/jbemmels_1.pd

Research Study of the Lived Experience of Alopecia Areata for Women During Early Adulthood.

University of Minnesota Ph.D. dissertation.June 2017. Major: Educational Psychology. Advisor: Patricia McCarthy Veach. 1 computer file (PDF); vi, 233 pages.Objectives: Alopecia areata (AA) is an autoimmune condition that causes baldness in men and women; however, it may be especially distressing for women given social standards and expectations for beauty. This sporadic condition can present with various extents of hair loss that unexpectedly relapse or remit across time. The present phenomenological study aimed to describe the lived experiences of early adult women with AA who developed it in pre-adolescence or adolescence, to provide greater understanding of the experience of having AA over time. Method: The present study is guided by phenomenological methods, including interpretive phenomenological analysis. Following in-depth, semi-structured interviews with six female participants ages 27-36 with current, active AA, who developed their AA between ages 10-16, data were transcribed and analyzed at an individual and general (i.e., cross case) level for themes. Results: Responses to initial awareness of AA or increasing hair loss were not uniform, with participants’ psychological experiences ranging from not being bothered to life-altering and devastating. Physical sensations and visual reminders of increased hair loss can pull participants out of their everyday experiences, with possible helplessness regarding inability to stop the loss. Losing hair was sometimes experienced as a deep emotional loss, and was sometimes so devastating that years felt “dark” or “lost.” Participants encountered uncertainty regarding when their hair might fall out, as well as unpredictability with others’ reactions. Participants often experienced normality with friends and family, but occasional rejection and derision from others led to certain spaces or situations feeling unsafe for revealing AA. Participants often concealed their AA with various approaches, including wigs or hair pins, which might lead to self-consciousness about the AA or wig being discovered. At some point, these routines become “automatic.” Disclosing about AA to others increased vulnerability and openness, which might have negative (e.g., fear of negative reactions) and positive (e.g., deeper relationships) implications. The threat of AA being incidentally discovered can be distressing even after decades of having AA, but for some, making an intentional choice to reveal AA (e.g., openly telling others, not wearing a wig) led to freedom and comfort with the tradeoff of possible increased attention through stares or questions. Discussion: AA impacts individuals’ lives in a variety of ways, and the impact can differ across time, situations, and relationships. AA can produce a great deal of distress that persists after more than a decade of living with it. For others, AA is less distressing. Psychologists and other providers might best serve individuals with AA by better assessing their individual experiences of the condition. Future research might investigate the process of how some individuals with AA come to greater acceptance of or appreciation for their AA

The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio

The advent of next-generation sequencing (NGS) technologies has transformed the way microsatellites are isolated for ecological and evolutionary investigations. Recent attempts to employ NGS for microsatellite discovery have used the 454, Illumina, and Ion Torrent platforms, but other methods including single-molecule real-time DNA sequencing (Pacific Biosciences or PacBio) remain viable alternatives. We outline a workflow from sequence quality control to microsatellite marker validation in three plant species using PacBio circular consensus sequencing (CCS). We then evaluate the performance of PacBio CCS in comparison with other NGS platforms for microsatellite isolation, through simulations that focus on variations in read length, read quantity and sequencing error rate. Although quality control of CCS reads reduced microsatellite yield by around 50%, hundreds of microsatellite loci that are expected to have improved conversion efficiency to functional markers were retrieved for each species. The simulations quantitatively validate the advantages of long reads and emphasize the detrimental effects of sequencing errors on NGS-enabled microsatellite development. In view of the continuing improvement in read length on NGS platforms, sequence quality and the corresponding strategies of quality control will become the primary factors to consider for effective microsatellite isolation. Among current options, PacBio CCS may be optimal for rapid, smallscale microsatellite development due to its flexibility in scaling sequencing effort, while platforms such as Illumina MiSeq will provide cost-efficient solutions for multispecies microsatellite projects.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108219/1/Na2014.pdf85Description of Na2014.pdf : main articl

Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

High-throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double-digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of FST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high-throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/136081/1/Nazareno et al. 2017a.pdfDescription of Nazareno et al. 2017a.pdf : Main articl

Tests of species‐specific models reveal the importance of drought in postglacial range shifts of a Mediterranean‐climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection

Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species‐specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade‐offs in functional traits, and local‐scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation. Specifically, we use ecological niche models (ENMs) to construct temporally dynamic landscapes where the processes invoked by each hypothesis are reflected by differences in local habitat suitabilities. These landscapes are used to simulate expected patterns of genetic variation under each model and evaluate the fit of empirical data from 13 microsatellite loci genotyped in 226 individuals from across the species range. Using approximate Bayesian computation (ABC), we obtain very strong support for two statistically indistinguishable models: a trade‐off model in which growth rate and drought tolerance drive habitat suitability and genetic structure, and a model based on the climatic niche estimated from a generic ENM, in which the variables found to make the most important contribution to the ENM have strong conceptual links to drought stress. The two most probable models for explaining the patterns of genetic variation thus share a common component, highlighting the potential importance of seasonal drought in driving historical range shifts in a temperate tree from a Mediterranean climate where summer drought is common.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134178/1/mec13804-sup-0001-Supinfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134178/2/mec13804.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134178/3/mec13804_am.pd

Canadian-American Jurisprudence on "Good Faith" Bargaining

Canadian-American Jurisprudence on « Good Faith » Bargainin

Survival near ice sheet margins for some, but not all, North American trees

Temperate species experienced dramatic range reductions during the Last Glacial Maximum, yet refugial populations from which modern populations are descended have never been precisely located. Climate-based models identify only broad areas of potential habitat, traditional phylogeographic studies provide poor spatial resolution, and pollen records for temperate forest communities are difficult to interpret and do not provide species-level taxonomic resolution. Here we harness signals of range expansion from large genomic datasets, using a simulation-based framework to infer the precise latitude and longitude of glacial refugia in two widespread, codistributed hickories (Carya spp.) and to quantify uncertainty in these estimates. We show that one species likely expanded from close to ice sheet margins near the site of a previously described macrofossil for the genus, highlighting support for the controversial notion of northern microrefugia. In contrast, the expansion origin inferred for the second species is compatible with classic hypotheses of distant displacement into southern refugia. Our statistically rigorous, powerful approach demonstrates how refugia can be located from genomic data with high precision and accuracy, addressing fundamental questions about long-term responses to changing climates and providing statistical insight into longstanding questions that have previously been addressed primarily qualitatively.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148529/1/Bemmels2019.pdf85Description of Bemmels2019.pdf : Main articl

Conceptual and empirical advances in Neotropical biodiversity research

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow\u27s ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life