Scholars@Duke
Paul S. Manos

Paul S. Manos

Professor in the Department of Biology
Biology
pmanos@duke.edu
Box 90338, Durham, NC 27708-0338
330 Bio Sci Bldg, Durham, NC 27708

Selected Publications

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes.

Journal Article Systematic biology · October 2024 Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hinde ... Full text Cite

A global blueberry phylogeny: Evolution, diversification, and biogeography of Vaccinieae (Ericaceae).

Journal Article Molecular phylogenetics and evolution · September 2024 Vaccinieae is a morphologically diverse and species-rich (∼1430 species) tribe in Ericaceae. Although the majority of diversity is tropical, Vaccinieae are best known for temperate crops (i.e., blueberries, cranberries, huckleberries, lingonberries) in Vac ... Full text Cite

Systematics and Evolution of Vaccinium Sect. Cyanococcus (Ericaceae): Progress and Prospects

Journal Article Rhodora · March 11, 2024 The true blueberries (Vaccinium sect. Cyanococcus; Ericaceae) comprise a clade of about nine to 24 species distributed mainly in eastern temperate North America, with one species reaching farther west. Despite extensive study, the systematics and evolution ... Full text Cite

STUDIES IN THE VASCULAR FLORA OF THE SOUTHEASTERN UNITED STATES. X

Journal Article Journal of the Botanical Research Institute of Texas · January 1, 2024 As part of ongoing work on the Flora of the Southeastern United States (Weakley & Southeastern Flora Team 2023) and related projects, as well as for general floristic, conservation, and scientific work in eastern North America, it is essential to document ... Full text Cite

VACCINIUM VIRGATUM (ERICACEAE): A SPECIES TO BE RECOGNIZED

Journal Article Journal of the Botanical Research Institute of Texas · January 1, 2024 Since its original publication in 1789, Vaccinium virgatum has been treated by most authors as an accepted species in V. sect. Cyanococcus. In the latest comprehensive taxonomic treatment of the section, however, it is treated as a synonym of the broadly c ... Full text Cite

A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus).

Journal Article American journal of botany · October 2022 PremiseThe true blueberries (Vaccinium sect. Cyanococcus; Ericaceae), endemic to North America, have been intensively studied for over a century. However, with species estimates ranging from nine to 24 and much confusion regarding species boundari ... Full text Cite

Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere.

Journal Article Nature communications · March 2022 Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks an ... Full text Cite

An updated infrageneric classification of the north american oaks (Quercus subgenus quercus): Review of the contribution of phylogenomic data to biogeography and species diversity

Journal Article Forests · June 1, 2021 The oak flora of North America north of Mexico is both phylogenetically diverse and species-rich, including 92 species placed in five sections of subgenus Quercus, the oak clade centered on the Americas. Despite phylogenetic and taxonomic progress on the g ... Full text Open Access Cite

Ascent of the Oaks.

Journal Article Scientific American · August 2020 Full text Cite

Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus).

Journal Article The New phytologist · May 2020 Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from the combination ... Full text Cite

Genomic landscape of the global oak phylogeny.

Journal Article The New phytologist · May 2020 The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak div ... Full text Cite

Comment on "Eocene Fagaceae from Patagonia and Gondwanan legacy in Asian rainforests".

Journal Article Science (New York, N.Y.) · November 2019 Wilf et al (Research Articles, 7 June 2019, eaaw5139) claim that Castanopsis evolved in the Southern Hemisphere from where it spread to its modern distribution in Southeast Asia. However, extensive paleobotanical records of Antarctica and Aus ... Full text Cite

One thousand plant transcriptomes and the phylogenomics of green plants.

Journal Article Nature · October 2019 Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetat ... Full text Open Access Cite

Genomic Identity of White Oak Species in an Eastern North American Syngameon

Journal Article Annals of the Missouri Botanical Garden · October 1, 2019 The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reali ... Full text Cite

Pervasive migration across rainforest and sandy coastal plain Aechmea nudicaulis (Bromeliaceae) populations despite contrasting environmental conditions.

Journal Article Molecular ecology · March 2018 Understanding the colonization of extreme marginal habitats and the relative roles of space and environment in maintaining peripheral populations remains challenging. Here, we leverage a system of pairs of rainforest and sandy coastal plain communities tha ... Full text Cite

Geographic range velocity and its association with phylogeny and life history traits in North American woody plants.

Journal Article Ecology and evolution · March 2018 The geographic ranges of taxa change in response to environmental conditions. Yet whether rates of range movement (biotic velocities) are phylogenetically conserved is not well known. Phylogenetic conservatism of biotic velocities could reflect similaritie ... Full text Cite

The role of diversification in community assembly of the oaks (Quercus L.) across the continental U.S.

Journal Article American journal of botany · March 2018 Premise of the studyEvolutionary and biogeographic history, including past environmental change and diversification processes, are likely to have influenced the expansion, migration, and extinction of populations, creating evolutionary legacy effe ... Full text Cite

Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia.

Journal Article Molecular phylogenetics and evolution · February 2018 The evolutionary history of Quercus section Cyclobalanopsis, a dominant lineage in East Asian evergreen broadleaved forests (EBLFs), has not been comprehensively studied using molecular tools. In this study, we reconstruct the first comprehensive phylogeny ... Full text Cite

Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity.

Journal Article The New phytologist · January 2018 Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate fores ... Full text Open Access Cite

The evolution and diversification of the red oaks of the California Floristic Province (Quercus section Lobatae, series Agrifoliae).

Journal Article American journal of botany · October 2017 Premise of the studyThe California Floristic Province (CA-FP) is a unique and diverse region of floral endemism, yet the timing and nature of divergence and diversification of many lineages remain underexplored. We seek to elucidate the evolutiona ... Full text Cite

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus).

Journal Article Genome · September 2017 The emergence of next generation sequencing has increased by several orders of magnitude the amount of data available for phylogenetics. Reduced representation approaches, such as restriction-sited associated DNA sequencing (RADseq), have proven useful for ... Full text Cite

A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny.

Journal Article Genome · September 2017 Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticula ... Full text Cite

Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America.

Journal Article Genome · September 2017 Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obv ... Full text Cite

A genetic legacy of introgression confounds phylogeny and biogeography in oaks.

Journal Article Proceedings. Biological sciences · May 2017 Oaks (Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks ... Full text Cite

Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences.

Journal Article PloS one · January 2017 The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants th ... Full text Cite

Evidence for genetic erosion of a California native tree, Platanus racemosa, via recent, ongoing introgressive hybridization with an introduced ornamental species

Journal Article Conservation Genetics · June 1, 2016 When non-native, genetically diverse species are introduced, hybridization with native congeners may erode the genetic composition of local species, perhaps even resulting in extinction. While such events may lead to adverse consequences at the community a ... Full text Cite

Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach.

Journal Article Molecular ecology · July 2015 The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North Ame ... Full text Cite

Biogeographic analysis of the woody plants of the Southern Appalachians: Implications for the origins of a regional flora.

Journal Article American journal of botany · May 2015 Premise of the studyWe investigated the origins of 252 Southern Appalachian woody species representing 158 clades to analyze larger patterns of biogeographic connectivity around the northern hemisphere. We tested biogeographic hypotheses regarding ... Full text Open Access Cite

A framework phylogeny of the American oak clade based on sequenced RAD data.

Journal Article PloS one · January 2014 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 phyloge ... Full text Cite

Limited hybridization across an edaphic disjunction between the gabbro-endemic shrub Ceanothus roderickii (Rhamnaceae) and the soil-generalist Ceanothus cuneatus.

Journal Article American journal of botany · September 2013 UnlabelledPremise of the studyHybridization is thought to have played an important role in diversification of the speciose shrub genus Ceanothus; putative hybrid species have been described, and data suggest that intrinsic barriers may no ... Full text Cite

Genomics of Fagaceae

Journal Article Tree Genetics and Genomes · June 1, 2012 An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8-10 genera. Usi ... Full text Cite

Diversification of Ceanothus (Rhamnaceae) in the California Floristic province

Journal Article International Journal of Plant Sciences · November 1, 2011 High diversity and endemism in the California Floristic Province (CFP) are an alleged response to the late Cenozoic advent of Mediterranean-type climate in this region. Ceanothus comprises two divergent subgenera with centers of diversity in the CFP. We re ... Full text Cite

Host density drives the postglacial migration of the tree parasite, Epifagus virginiana.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · September 2010 To survive changes in climate, successful species shift their geographic ranges to remain in suitable habitats. For parasites and other highly specialized species, distributional changes not only are dictated by climate but can also be engineered by their ... Full text Cite

Natural history, distribution, phylogenetic relationships, and conservation of Central American black walnuts (Juglans sect. Rhysocaryon)

Journal Article Journal Torrey Botanical Society · February 2009 STONE, D. E., S.-H. OH, E.A. TRIPP (Department of Biology, Duke University, Durham, NC 27708), L. E. RI´OS G. (Oficina Te´cnica en Biodiversidad, Consejo Nacional de Areas Protegidas, 5 av. 6-06, zona 1, Edificio del IPM, 7 mo. nivel, Guatemala, Guatemala) ... Cite

Inferring long-distance dispersal and topographic barriers during post-glacial colonization from the genetic structure of red maple (Acer rubrum L.) in New England

Journal Article Journal of Biogeography · September 1, 2008 Aim: This study aims to assess the role of long-distance seed dispersal and topographic barriers in the post-glacial colonization of red maple (Acer rubrum L.) using chloroplast DNA (cpDNA) variation, and to understand whether this explains the relatively ... Full text Cite

Is floral specialization an evolutionary dead-end? Pollination system transitions in Ruellia (Acanthaceae).

Journal Article Evolution; international journal of organic evolution · July 2008 Pollination systems frequently reflect adaptations to particular groups of pollinators. Such systems are indicative of evolutionary specialization and have been important in angiosperm diversification. We studied the evolution of pollination systems in the ... Full text Cite

Hydraulic traits are influenced by phylogenetic history in the drought-resistant, invasive genus Juniperus (Cupressaceae).

Journal Article American journal of botany · March 2008 In the conifer genus Juniperus (Cupressaceae), many species are increasing rapidly in distribution, abundance, and dominance in arid and semiarid regions. To help understand the success of junipers in drier habitats, we studied hydraulic traits associated ... Full text Cite

Molecular phylogeny of Nyctaginaceae: taxonomy, biogeography, and characters associated with a radiation of xerophytic genera in North America.

Journal Article American journal of botany · May 2007 The four o'clock family (Nyctaginaceae) has a number of genera with unusual morphological and ecological characters, several of which appear to have a "tendency" to evolve repeatedly in Nyctaginaceae. Despite this, the Nyctaginaceae have attracted little a ... Full text Cite

Comparative phylogeography of unglaciated eastern North America.

Journal Article Molecular ecology · December 2006 Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern ... Full text Cite

Untangling Physalis (Solanaceae) from the physaloids: A two-gene phylogeny of the physalinae

Journal Article Systematic Botany · January 1, 2005 Physalis (75+ species, Solanaceae) is most diverse in Mexico, with only the type, P. alkekengi, native to the Old World. Interspecific relationships are poorly known, and despite the distinctive inflated fruiting calyces, generic limits remain uncertain. S ... Full text Cite

Molecular indicators of tree migration capacity under rapid climate change

Journal Article Ecology · January 1, 2005 Recent models and analyses of paleoecological records suggest that tree populations are capable of rapid migration when climate warms. Fossil pollen is commonly interpreted as suggesting that the range of many temperate tree species expanded at rates of 10 ... Full text Cite

Systematics of Ipomoea subgenus Quamoclit (Convolvulaceae) based on ITS sequence data and a Bayesian phylogenetic analysis.

Journal Article American journal of botany · August 2004 A Bayesian phylogenetic analysis of 36 Ipomoea species using sequence data from the internal transcribed spacer region was compared with classification schemes based on traditional methods and a previously published cpDNA restriction fragment length polymo ... Full text Cite

Phylogenetic relationships in Fagales based on DNA sequences from three genomes

Journal Article International Journal of Plant Sciences · January 1, 2004 Nucleotide sequences of six regions from three plant genomes - trnL-F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S rDNA (nuclear) - were used to analyze inter- and infrafamilial relationships of Fagales. All 31 extant genera representing eight famili ... Full text Cite

Phylogenetic relationships of the perianthless Piperales: Reconstructing the evolution of floral development

Journal Article International Journal of Plant Sciences · January 1, 2004 The perianthless members of the Piperales are unique among the basal lineages of angiosperms because they are mainly herbaceous plants with over 2000 species possessing highly reduced flowers. There have been several attempts to address the evolution of th ... Full text Cite

The phylogeny, evolution, and classification of the genus Globba and tribe Globbeae (Zingiberaceae): appendages do matter.

Journal Article American journal of botany · January 2004 The genus Globba (100 species) is one of the largest genera in the primarily tropical Zingiberaceae. Globba along with the small genera Gagnepainia, Hemiorchis, and Mantisia comprise the Globbeae, one of the two tribes of subfamily Zingiberoideae. Traditio ... Full text Cite

Biogeography of Exostema (Rubiaceae) in the Caribbean region in light of molecular phylogenetic analyses

Journal Article Systematic Botany · April 1, 2003 Exostema (Rubiaceae) comprises 25 neotropical woody species, ranging from western South America and Mesoamerica to the West Indies, with 19 species occurring in Cuba and Hispaniola. Biogeographical hypotheses based upon a phylogenetic analysis of morpholog ... Cite

Phylogeography of the Southeast Asian stone oaks (Lithocarpus)

Journal Article Journal of Biogeography · February 1, 2003 Aim: To describe current geographical patterns of genetic diversity and infer the historical population dynamics of the stone oaks (Lithocarpus) in Southeast Asia. Location: We sampled three populations in Indochina: (1) Yunnan province, China; (2) Pyin Oo ... Full text Cite

An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference.

Journal Article Systematic biology · October 2002 The objective of this study was to obtain a quantitative assessment of the monophyly of morning glory taxa, specifically the genus Ipomoea and the tribe Argyreieae. Previous systematic studies of morning glories intimated the paraphyly of Ipomoea by sugges ... Full text Cite

Phylogenetic analysis of Ipomoea, Argyreia, Stictocardia, and Turbina suggests a generalized model of morphological evolution in morning glories

Journal Article Systematic Botany · October 11, 2001 We tested the phylogenetic hypothesis that the circumscription of the genus Ipomoea comprises all members of Hallier's historical taxon, subfamily "Echinoconiae", including Argyreia, Astripomoea, Lepistemon, Rivea, Stictocardia, and Turbina. Support for th ... Cite

Phylogeny and patterns of floral diversity in the genus Piper (Piperaceae).

Journal Article American journal of botany · April 2001 With ∼1000 species distributed pantropically, the genus Piper is one of the most diverse lineages among basal angiosperms. To rigorously address the evolution of Piper we use a phylogenetic analysis of sequences of the internal transcribed spacers (ITS) of ... Full text Cite

Molecular and morphological analyses of Bryopsis (Bryopsidales, Chlorophyta) from the western North Atlantic and Caribbean

Journal Article Phycologia · January 1, 2001 Three species of Bryopsis have commonly been reported from the western North Atlantic, but continuous morphological variation has often confounded specimen identification. This study evaluates the utility of the coding and non-coding sequences of the psbB ... Full text Cite

Systematics of Fagaceae: Phylogenetic tests of reproductive trait evolution

Journal Article International Journal of Plant Sciences · January 1, 2001 The family Fagaceae includes nine currently recognized genera and ca. 1000 species, making it one of the largest and most economically important groups within the order Fagales. In addition to wide variation in cupule and fruit morphology, polymorphism in ... Full text Cite

Progress in Northern Hemisphere phytogeography: An introduction

Journal Article International Journal of Plant Sciences · January 1, 2001 Full text Cite

Evolution, phylogeny, and systematics of the Juglandaceae

Journal Article Annals of the Missouri Botanical Garden · January 1, 2001 A comprehensive systematic investigation was conducted on the extant Juglandaceae based on 25 species representing a broad sample of generic and infrageneric diversity. A total of 206 phylogenetically informative characters derived from morphological, chem ... Full text Cite

The historical biogeography of Fagaceae: Tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere

Journal Article International Journal of Plant Sciences · January 1, 2001 The angiosperm family Fagaceae is a central element of several distinct community types throughout the Northern Hemisphere and a prime candidate for modern biogeographic analysis. The rich fossil record for the family provides an unparalleled source to com ... Full text Cite

The Bornean Lithocarpus Bl. section Synaedrys (Lindl.) Barnett (Fagaceae): Its circumscription and description of a new species

Journal Article Botanical Journal of the Linnean Society · January 1, 2000 The Bornean species of Lithocarpus Bl. section Synaedrys (Lindl.) Barnett (Fagaceae) are discussed in terms of their unifying characteristics, and keys to the species are provided. A novel morphological feature present in the genus, where the seed in the m ... Full text Cite

Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae).

Journal Article Molecular phylogenetics and evolution · August 1999 Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the ... Full text Cite

Phylogenetic systematics of Ipomoea (Convolvulaceae) based on ITS and Waxy sequences

Journal Article Systematic Botany · January 1, 1999 Ipomoea is a large and complex genus containing over 600 species of vines and shrubs widely distributed throughout the tropics and subtropics. The phylogeny of 40 species representing the three currently recognized subgenera and nine sections within the ge ... Full text Cite

Phylogenetic analyses of "higher" Hamamelididae based on plastid sequence data.

Journal Article American journal of botany · October 1997 Phylogenetic relationships were examined within the "higher" Hamamelididae using 21 species representing eight families and related outgroups. Chloroplast DNA sequences encoding the matK gene (/1 kilobase) provided 258 informative nucleotide sites. Phyloge ... Full text Cite

Systematics of Nothofagus (Nothofagaceae) based on rDNA spacer sequences (ITS): taxonomic congruence with morphology and plastid sequences.

Journal Article American journal of botany · August 1997 Phylogenetic relationships were examined within the southern beech family Nothofagaceae using 22 species representing the four currently recognized subgenera and related outgroups. Nuclear ribosomal DNA sequences encoding the 5.8s rRNA and two flanking int ... Full text Cite