New interpretations of fine-scale spatial genetic structure

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72211/1/j.1365-294X.2008.03728.x.pd

Polymorphic microsatellite markers for a wind‐dispersed tropical tree species, Triplaris cumingiana (Polygonaceae)

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141549/1/aps31400051.pd

A similar phylogeographical structure among sympatric North American birches (Betula) is better explained by introgression than by shared biogeographical history

AimA comparative analysis of the chloroplast (cp) DNA structure of eastern North American birches (Betula) was undertaken to infer the impacts of Quaternary climate change on the phylogeographical structure of these species.LocationEastern North America.MethodsGenetic variation in chloroplast microsatellites (cpSSRs) and the psbA–trnH intergenic spacer in Betula papyrifera, Betula alleghaniensis and Betula lenta was analysed in samples from 65, 80 and 12 populations, respectively. Co‐occurring Betula uber, Betula populifolia and Betula cordifolia were also sampled to examine haplotype relationships and account for potential introgression. Haplotype networks, Bayesian analysis and comparisons of RST and GST values were used to evaluate the phylogeographical structure. Genetic diversity within and among species was compared using rarefaction analysis.ResultsThe two most widespread species, B. papyrifera and B. alleghaniensis, showed high levels of haplotype diversity, while the Appalachian endemic B. lenta possessed a single haplotype. Bayesian analysis revealed three main phylogeographical groups for B. papyrifera and four groups for B. alleghaniensis, and these two species showed extensive regional haplotype sharing and a high introgression ratio.Main conclusionsWe postulate that at least three separate refugia contributed to the recolonization of B. papyrifera and B. alleghaniensis within eastern North America, while B. lenta appears to have recolonized from a single refugium. A high haplotype diversity of B. papyrifera and B. alleghaniensis in the Great Lakes region may reflect biogeographical contact between eastern and western lineages, with the potential influence of periglacial refugia. Similar phylogeographical patterns in the distantly related B. papyrifera and B. alleghaniensis represent a geographical turnover of the same locally shared haplotypes, pointing to introgression rather than shared biogeographical history as the mechanism. Although similar phylogeographical patterns are often interpreted as evidence for common biogeographical histories, our study demonstrates that such patterns can also arise through introgression.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110577/1/jbi12394.pd

Diversification history of Neotropical Lecythidaceae, an ecologically dominant tree family of Amazon rain forest

The Neotropical subfamily of Lecythidaceae (Lecythidoideae) is a clade of 10 genera with an estimated number of 232 species. Lecythidaceae is the third most abundant family of trees in Amazon forests, and its most diverse genus, Eschweilera (ca. 100 species) is the most abundant genus of Amazon trees. In this chapter we explore the diversification history of the Lecythidoideae through space and time in the Neotropics. We inferred a time-calibrated phylogeny of 118 species, which we used to reconstruct the biogeographic origins of Lecythidoideae and its main clades. To test for significant changes of speciation rates in the subfamily, we performed a diversification analysis. Our analysis dated the crown clade of Lecythidoideae at 46 Ma (95% CI 1⁄4 36.5–55.9 Ma) and the stem age at 62.7 Ma (95% CI 1⁄4 56.7–68.9 Ma), suggesting dispersal from the paleotropics long after the Gondwana breakup. Most major crown clades in the Lecythidoideae (Grias, Gustavia, Eschweilera, Couroupita, Couratari, and all Lecythis and Eschweilera subclades) differentiated during the Miocene (ca. 5.3–23 Ma). The Guayana floristic region (Guiana Shield + north-central Amazon) is the inferred ancestral range for 8 out of the 18 Lecythidoideae clades (129 species, ~55%), highlighting the region’s evolutionary importance, especially for the species-rich Bertholletia clade, which includes the genera Eschweilera, Lecythis, Corythophora and Bertholletia. Our results indicate that the Bertholletia clade colonized the Trans-Andean region at least three times in the last 10 Ma. We found no significant changes in the rate of diversification inside Lecythidoideae over the Cenozoic, and found no evidence of increased speciation during the Pleistocene. Lecythidoideae has diversified not in pulses, but in a pattern of steady accumulation, akin to a museum model of diversification.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155560/1/Vargas2020_Chapter_DiversificationHistoryOfNeotro.pdf85Description of Vargas2020_Chapter_DiversificationHistoryOfNeotro.pdf : Main articl

Burton V. Barnes as a forest botanist

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/120432/1/Dick2016_Barnes_Tribute.pdfDescription of Dick2016_Barnes_Tribute.pdf : Main articl

Linear Actuator System for the NASA Docking System

The Linear Actuator System (LAS) is a major sub-system within the NASA Docking System (NDS). The NDS Block 1 will be used on the Boeing Crew Space Transportation (CST-100) system to achieve docking with the International Space Station. Critical functions in the Soft Capture aspect of docking are performed by the LAS. This paper describes the general function of the LAS, the system's key requirements and technical challenges, and the development and qualification approach for the system

Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144266/1/aps31151_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144266/2/aps31151.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144266/3/aps31151-sup-0001-AppendixS1.pd

Extreme long-distance dispersal of the lowland tropical rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics

Many tropical tree species occupy continental expanses of rainforest and flank dispersal barriers such as oceans and mountains. The role of long-distance dispersal in establishing the range of such species is poorly understood. In this study, we test vicariance hypotheses for range disjunctions in the rainforest tree Ceiba pentandra , which is naturally widespread across equatorial Africa and the Neotropics. Approximate molecular clocks were applied to nuclear ribosomal [ITS (internal transcribed spacer)] and chloroplast ( psb B- psb F) spacer DNA sampled from 12 Neotropical and five West African populations. The ITS ( N  = 5) and psb B- psb F ( N  = 2) haplotypes exhibited few nucleotide differences, and ITS and psb B- psb F haplotypes were shared by populations on both continents. The low levels of nucleotide divergence falsify vicariance explanations for transatlantic and cross-Andean range disjunctions. The study shows how extreme long-distance dispersal, via wind or marine currents, creates taxonomic similarities in the plant communities of Africa and the Neotropics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71417/1/j.1365-294X.2007.03341.x.pd

Tropical mountain cradles of dry forest diversity

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/83302/1/Dick2005.pd

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