22 Works

Pronounced genetic separation among varieties of the Primula cusickiana species complex, a Great Basin endemic

Austin Koontz, William Pearse & Paul Wolf
Distinguishing between populations with strong genetic structure and unique species is a common challenge in systematics, especially for taxa occurring in fragmented habitats where allopatric speciation may be widespread and distinct groups may be morphologically similar. Such is often the case with species complexes across sky island environments. In these scenarios, biogeography may help to explain the taxonomic relations between species complex members, and restriction site-associated DNA (RAD) sequencing methods are commonly used to compare...

The invasion paradox dissolves when using phylogenetic and temporal perspectives

Adrienne Ernst, Rebecca Barak, Andrew Hipp, Andrea Kramer, Hannah Marx & Daniel Larkin
1. Elton’s prediction that higher biodiversity leads to denser niche-packing and thus higher community resistance to invasion has long been studied, with species richness as the predominant measure of diversity. However, few studies have explored how phylogenetic and functional diversity, which should represent niche space more faithfully than taxonomic diversity, influence community invasibility, especially across longer time frames and over larger spatial extents. 2. We used a 15-year, 150-site grassland dataset to assess relationships between...

Data from: Phylogenetic measures of plant communities show long-term change and impacts of fire management in tallgrass prairie remnants

Daniel J. Larkin, Andrew L. Hipp, Jens Kattge, William Prescott, Rebecca K. Tonietto, Sarah K. Jacobi & Marlin L. Bowles
1. Phylogenies are increasingly incorporated into ecological studies on the basis that evolutionary relatedness broadly correlates with trait similarity. However, phylogenetic approaches have rarely been applied to monitoring long-term community change or guiding management. 2. We analysed a 25-year resampling data set (1976–2001) of 41 tallgrass prairie remnants (Illinois, USA) to test for phylogenetic signals of plant community structure, change, environmental associations, fire management and functional traits. A community phylogeny was constructed using GenBank sequences...

Data from: Chromosome number evolves independently of genome size in a clade with non-localized centromeres (Carex: Cyperaceae)

Kyong-Sook Chung, Andrew L. Hipp & Eric H. Roalson
The effects of chromosome rearrangement on genome size are poorly understood. While chromosome duplications and deletions have predictable effects on genome size, chromosome fusion, fission, and translocation do not. In this study, we investigate genome size and chromosome number evolution in 87 species of Carex, one of the most species-rich genera of flowering plants and one that has undergone an exceptionally high rate of chromosome rearrangement. Using phylogenetic generalized least squares regression, we find that...

Data from: Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

Gang Wang, Xingtan Zhang, Edward Herre, Charles Cannon, Doyle McKey, Carlos Machado, Wen-Bin Yu, Michael Arnold, Rodrigo Pereira, Ray Ming, Yi-Fei Liu, Yibin Wang, Dongna Ma & Jin Chen
Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and...

Repeated parallel losses of inflexed stamens in Moraceae: phylogenomics and generic revision of the tribe Moreae and the reinstatement of the tribe Olmedieae (Moraceae)

Elliot Gardner
We present a densely-sampled phylogenomic study of the mulberry tribe (Moreae, Moraceae), an economically important clade with a global distribution, revealing multiple losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed stamens facilitate ballistic pollen release and are associated with wind pollination, and the results presented here suggest that losses of this character state may have evolved repeatedly in Moraceae. Neither Moreae nor several of its major genera (Morus, Streblus, Trophis) were...

Data from: A framework phylogeny of the American oak clade based on sequenced RAD data

Andrew L. Hipp, Deren A. R. Eaton, Jeannine Cavender-Bares, Elisabeth Fitzek, Rick Nipper & Paul S. Manos
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters....

Data from: Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)

Andrew A. Crowl, Paul S. Manos, John D. McVay, Alan R. Lemmon, Emily Moriarty Lemmon & Andrew L. Hipp
• Botanists have long recognized interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterized, and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. • Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci....

Data from: Native plant diversity increases herbivory to non-natives

Ian S. Pearse & Andrew L. Hipp
There is often an inverse relationship between the diversity of a plant community and the invasibility of that community by non-native plants. Native herbivores that colonize novel plants may contribute to diversity–invasibility relationships by limiting the relative success of non-native plants. Here, we show that, in large collections of non-native oak trees at sites across the USA, non-native oaks introduced to regions with greater oak species richness accumulated greater leaf damage than in regions with...

Phylogeny, biogeography, and classification of the elms (Ulmus)

Andrew Hipp, Alan Whittemore, Ryan S. Fuller, Bethany H. Brown, Marlene Hahn, Linus Gog & Jaime A. Weber
A RAD-seq phylogeny is presented for the genus Ulmus, and a revised infrageneric classification is given, with keys, descriptions, and range maps for the subgenera and sections. The previously accepted classification was based on a cpDNA phylogeny, but several well-marked clades in the chloroplast phylogeny are not recovered in the RAD-seq phylogeny and do not seem to represent valid clades in the organismal phylogeny. Ordination and STRUCTURE analysis support a broad species concept in Ulmus...

Range shifts in butternut, a rare, endangered tree, in response to past climate and modern conditions

Emily Schumacher, Alissa Brown, Martin Williams, Jeanne Romero-Severson, Tannis Beardmore & Sean Hoban
Aim: Range shifts are a key process that determine species distributions and genetic patterns. A previous investigation reported that Juglans cinerea (butternut) has lower genetic diversity at higher latitudes, hypothesized to be the result of range shifts following the last glacial period. However, genetic patterns can also be impacted by modern ecogeographic conditions. Therefore, we re-investigate genetic patterns of butternut with additional northern population sampling, hindcasted species distribution models, and fossil pollen records to clarify...

Species packing and the latitudinal gradient in local beta-diversity

Ke Cao, Richard Condit, Xiangcheng Mi, Lei Chen, Wubing Xu, David F. R. P. Burslem, Chunrong Cai, Min Cao, Li-Wan Chang, Chengjin Chu, Hu Du, Sisira Ediriweera, C. S. V. Gunatilleke, I. U. A. N. Gunatilleke, Zhanqing Hao, Jinbo Li, Guangze Jin, Buhang Li, Yankun Liu, Yide Li, Michael J. O'Brien, Xiujuan Qiao, Hongwei Ni, Guochun Shen, Xihua Wang … & Jens-Christian Svenning
The decline in species richness at higher latitudes is among the most fundamental patterns in ecology. Whether changes in species composition across space (beta-diversity) contribute to this gradient of overall local species richness (gamma diversity) remains hotly debated. Previous studies that failed to resolve the issue suffered from a well-known tendency for small samples in areas with high gamma-diversity to have inflated measures of beta-diversity. We provide here a novel analytical test, using beta-diversity metrics...

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

Elliot Gardner, Matthew Johnson, Joan Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Sahromi Sahromi, Norman Wickett & Nyree Zerega
We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the...

Data from: A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Elisabeth Fitzek, Adline Delcamp, Erwan Guichouc, Marlene Hahn, Matthew Lobdell, Andrew L. Hipp & Erwan Guichoux
DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restriction-site associated DNA sequencing (RAD-seq) to develop an economical single-nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with post-clustering bioinformatic tools to generate a list of 291 potential...

Even more oak species in Mexico? Genetic structure and morphological differentiation support the presence of at least two specific entities within Quercus laeta

Saddan Morales-Saldaña, Ken Oyama, Susana Valencia Ávalos, Efraín Tovar Sánchez, Andrew Hipp & Antonio González Rodríguez
Differentiation among populations, sometimes despite ongoing gene exchange, is a key step in speciation. Therefore, comparison of intra- and interspecific differentiation patterns is of great significance to understanding speciation. The genus Quercus is an interesting system to test speciation models in the presence of gene flow, due to its weak interspecific reproductive barriers. The aim of the present study was to characterize the degree and pattern of morphological and genetic differentiation among different morphotypes in...

Data from: Molecular and morphological perspectives on the circumscription of Carex section Heleoglochin (Cyperaceae)

Ana Molina, Kyong-Sook Chung & Andrew L. Hipp
Vignea is the only monophyletic subgenus in the genus Carex (Cyperaceae), comprising nearly 300 members grouped into 19–28 sections. Molecular studies have demonstrated that most of these sections are polyphyletic. Here, we seek to clarify the relationships among species in section Heleoglochin based on phylogenetic and morphological analyses. We analyzed sequence data using nuclear ribosomal DNA internal and external transcriber spacer regions of 60 representative specimens of sect. Heleoglochin, representing the full geographic range of...

Data from: Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes

Andrew Hipp, Paul Rothrock, Richard Whitkus & Jaime Weber
Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes—chromosomes in which centromeric activity is distributed along the length of the chromosome—have not. We collected chromosome number...

Data from: Global patterns of leaf defenses in oak species

Ian S. Pearse & Andrew L. Hipp
Plant defensive traits drive patterns of herbivory and herbivore diversity among plant species. Over the past 30 years, several prominent hypotheses have predicted the association of plant defenses with particular abiotic environments or geographic regions. We used a strongly supported phylogeny of oaks to test whether defensive traits of 56 oak species are associated with particular components of their climatic niche. Climate predicted both the chemical leaf defenses and the physical leaf defenses of oaks,...

Demographic rates and stature of tree species in 13 sub-tropical forests: annual growth, annual survival, annual recruitment >( 1 cm dbh), stature (max dbh)

Stephan Kambach, Richard Condit, Salomón Aguilar, Helge Bruelheide, Sarayudh Bunyavejchewin, Chia-Hao Chang-Yang, Yu-Yun Chen, George Chuyong, Stuart J. Davies, Sisira Ediriweera, Corneille E. N. Ewango, Edwino S. Fernando, Nimal Gunatilleke, Savitri Gunatilleke, Stephen P Hubbell, Akira Itoh, David Kenfack, Somboon Kiratiprayoon, Yi-Ching Lin, Jean-Remy Makana, Mohizah Bt. Mohamad, Nantachai Pongpattananurak, Rolando Pérez, Lillian Jennifer V. Rodriguez, I-Fang Sun … & Nadja Rüger
Organisms of all species must balance their allocation to growth, survival and recruitment. Among tree species, evolution has resulted in different life-history strategies for partitioning resources to these key demographic processes. Life-history strategies in tropical forests have often been shown to align along a trade-off between fast growth and high survival, i.e. the well-known fast-slow continuum. In addition, an orthogonal trade-off has been proposed between tall stature – resulting from fast growth and high survival...

Selection on convergent functional traits drives compositional divergence in a tallgrass prairie restoration experiment

Nisa Karimi & Andrew Hipp
1. Plant biodiversity is often partitioned into taxonomic diversity (species composition and abundance), phylogenetic diversity (breadth of evolutionary lineages) and functional diversity (resource‐use strategies or physical traits). Evaluating the effects and interplay of these dimensions can provide insights into how assembly processes drive compositional changes in plant communities. However, teasing apart the effects of different biodiversity dimensions is challenging in observational studies or retrospective analyses. 2. To evaluate how plant phylogenetic and trait history shape...

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

Lionel Di Santo, Sean Hoban, Thomas Parchman, Jessica Wright & Jill Hamilton
Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better-informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world’s rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the...

Data from: Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes

Andrew Hipp, Paul Rothrock, Richard Whitkus & Jaime Weber
Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes—chromosomes in which centromeric activity is distributed along the length of the chromosome—have not. We collected chromosome number...

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