Practical considerations for plant phylogenomics

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143756/1/aps31038_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143756/2/aps31038.pd

Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult

Using multiple, independent approaches to molecular species delimitation is advocated to accommodate limitations and assumptions of a single approach. Incongruence in delimitation schemes is a potential byâ product of employing multiple methods on the same data, and little attention has been paid to its reconciliation. Instead, a particular scheme is prioritized, and/or molecular delimitations are coupled with additional, independent lines of evidence that mitigate incongruence. We advocate that incongruence within a line of evidence should be accounted for before comparing across lines of evidence that can themselves be incongruent. Additionally, it is not uncommon for empiricists working in nonmodel systems to be dataâ limited, generating some concern for the adequacy of available data to address the question of interest. With conservation and management decisions often hinging on the status of species, it seems prudent to understand the capabilities of approaches we use given the data we have. Here, we apply two molecular species delimitation approaches, spedeSTEM and BPP, to the Castilleja ambigua (Orobanchaceae) species complex, a relatively young plant lineage in western North America. Upon finding incongruence in our delimitation, we employed a post hoc simulation study to examine the power of these approaches to delimit species. Given the data we collected, we find that spedeSTEM lacks the power to delimit while BPP is capable, thus allowing us to address incongruence before proceeding in delimitation. We suggest post hoc simulation studies like this compliment empirical delimitation and serve as a means of exploring conflict within a line of evidence and dealing with it appropriately.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144255/1/mec14590_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144255/2/mec14590.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144255/3/mec14590-sup-0001-DataS1-S7.pd

Oligocene niche shift, Miocene diversification – cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae)

Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results: To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions: Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change

Primers for Castilleja and their utility across Orobanchaceae: I. Chloroplast primers1

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141726/1/aps31700020.pd

Primers for Castilleja and their Utility Across Orobanchaceae: I. Chloroplast Primers

Premise of the study: Chloroplast primers were developed from genomic data for the taxonomically challenging genus Castilleja. We further tested the broader utility of these primers across Orobanchaceae, identifying a core set of chloroplast primers amplifying across the clade.Methods and Results: Using a combination of three low-coverage Castilleja genomes and sequence data from 12 Castilleja plastomes, 76 primer combinations were specifically designed and tested for Castilleja. The primers targeted the most variable portions of the plastome and were validated for their applicability across the clade. Of these, 38 primer combinations were subsequently evaluated in silico and then validated across other major clades in Orobanchaceae.Conclusions: These results demonstrate the utility of these primers, not only across Castilleja, but for other clades in Orobanchaceae— particularly hemiparasitic lineages—and will contribute to future phylogenetic studies of this important clade of parasitic plants

The origin and diversification of the hyperdiverse flora in the Chocó biogeographic region

Extremely high levels of plant diversity in the American tropics are derived from multiple interactions between biotic and abiotic factors. Previous studies have focused on macro-evolutionary dynamics of the Tropical Andes, Amazonia, and Brazil’s Cerrado and Atlantic forests during the last decade. Yet, other equally important Neotropical biodiversity hotspots have been severely neglected. This is particularly true for the Chocó region on the north-western coast of South and Central America. This geologically complex region is Earth’s ninth most biodiverse hotspot, hosting approximately 3% of all known plant species. Here, we test Gentry’s [1982a,b] hypothesis of a northern Andean-Central American Pleistocene origin of the Chocoan flora using phylogenetic reconstructions of representative plant lineages in the American tropics. We show that plant diversity in the Chocó is derived mostly from Andean immigrants. Contributions from more distant biogeographical areas also exist but are fewer. We also identify a strong floristic connection between the Chocó and Central America, revealed by multiple migrations into the Chocó during the last 5 Ma. The dated phylogenetic reconstructions suggest a Plio-Pleistocene onset of the extant Chocó flora. Taken together, these results support to a limited extend Gentry’s hypothesis of a Pleistocene origin and of a compound assembly of the Chocoan biodiversity hotspot. Strong Central American–Chocoan floristic affinity may be partly explained by the accretion of a land mass derived from the Caribbean plate to north-western South America. Additional densely sampled phylogenies of Chocoan lineages also well represented across the Neotropics could enlighten the role of land mass movements through time in the assembly of floras in Neotropical biodiversity hotspots

Phylogenomic Insights into the Radiation of an Andean Group of Plants

This dissertation focuses on the evolutionary history of the Neobartsia clade of the plant genus Bartsia (Orobanchaceae) distributed throughout the high elevation p�ramo ecosystem in the Andes. This group of plants was the subject of a detailed taxonomic study in the 1990's, as well as various phylogenetic studies at higher taxonomic levels. However, the work presented in this dissertation constitutes the most comprehensive study of the group so far. I conducted extensive fieldwork throughout the Andes and was able to sample every species described to date, including multiple individuals per species for many, and I have used these collections to elucidate phylogenetic relationships among closely related genera, and between the ~45 species in the clade. My molecular systematic work was accompanied by comparative phylogenetic studies focused on the time of divergence, historical biogeography, and the rate of diversification of the group, which showed that the clade is the result of an ongoing recent and rapid radiation that began ~3 million years ago - a time period when the northern Andes had the necessary elevation to generate alpine conditions. It was clear from these studies, that the genetic diversity within Neobartsia was low, given the young age of the genus, and therefore, I began to focus on developing genomic approaches to generate large amounts of phylogenetic data, both efficiently and cost effectively. This last part of my dissertation resulted in two genomic methods being developed, one for sequencing complete chloroplast genomes, and one for generating targeted subgenomic datasets, which were used to generate the data necessary to elucidate interspecific relationships. Finally, I revised the taxonomy of the clade and its closely allied genera to reflect these phylogenetic results, alleviating a history of taxonomic instability by elevating the South American Bartsia clade to the newly formed genus Neobartsia, thereby recognizing its unique evolutionary history.Thesis (Ph.D., Biology)--University of Idaho, May 201

Molecular Phylogeny for the Colombian species of páramo, for the genera Bartsia and Castilleja (Orobanchaceae)

<p>Thesis B.Sc. Biology, Universidad de los Andes, Bogotá – Colombia</p

Phylogenomics of the Andean Plant genus Burmeistera (Campanulaceae)

Oral presentation at the Evolution Meeting 2017 (Portland) describing my work on the phylogenomics of the plant genus Burmeistera (Campanulaceae)