Jacob B. Landis

Jacob B. Landis
Cornell University | CU · School of Integrative Plant Sciences

About

212
Publications
25,483
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1,002
Citations
Additional affiliations
July 2017 - June 2020
University of California, Riverside
Position
  • Fellow

Publications

Publications (212)
Article
Full-text available
Arecaceae is a species-rich clade of Arecales, while also being regarded as a morphologically diverse angiosperm family with numerous species having significant economic, medicinal, and ornamental value. Although in-depth studies focused on the chloroplast structure of Arecaceae, as well as inferring phylogenetic relationships using gene fragments,...
Article
Full-text available
Selection together with variation in floral traits can act to mold floral form, often driven by a plant's predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its e...
Preprint
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The genus Lonicera L. is widely distributed and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly known. In this study, we sampled 37 accessions of Lonicera, covering four sectio...
Preprint
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Asexual lineages are perceived to be short-lived on evolutionary timescales due to accumulation of deleterious mutations. Hence reports for exceptional cases of putative "ancient asexual" species usually raise doubts about whether such species are recently derived or engage in some undocumented sexual reproduction. However, there have been few stud...
Article
Background and Aims Hybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles...
Article
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Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from n...
Article
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Aims The tropical niche conservatism (TNC) hypothesis and the out of the tropics (OTT) hypothesis propose mechanisms generating patterns of species diversity across warm‐to‐cold thermal gradients at large spatial scales. These two hypotheses both integrate ecological and biogeography‐related evolutionary factors, but they predict opposite patterns...
Article
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Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a y...
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Background Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic–conti...
Article
Aim Natural selection typically results in the homogenization of reproductive traits, reducing natural variation within populations; thus, highly polymorphic species present unresolved questions regarding the mechanisms that shape and maintain gene flow given a diversity of phenotypes. We used an integrative framework to characterize phenotypic div...
Preprint
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Premise of this study: Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and...
Article
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Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Tran...
Article
Full-text available
Background The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the Large Single-Copy (LSC) region. Halesia and Pterostyrax are not supported...
Article
Background and Aims Abelia (Caprifoliaceae) is a small genus with five species, including one artificial hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, Taiwan Island and the Ryukyu Islands, providing a model system to explore the mechanisms of species dispersal in the East Asian flora. However, the...
Article
Full-text available
Evolutionary radiations have intrigued biologists for more than a century, yet our understanding of the drivers of radiating diversification is still limited. We investigate the roles of environmental and species-intrinsic factors in driving the rapid radiation of Saussurea (Asteraceae) by deploying a number of palaeoenvironment-, diversity- and tr...
Data
Review history of Macroevolutionary pattern of Saussurea (Asteraceae) provides insights into the drivers of radiating diversification
Preprint
Full-text available
Background and Aims Hybridization is a common and important force in plant evolution. One of its outcomes is introgression - the transfer of small genomic regions from one taxon to another by hybridization and repeated backcrossing. This process is believed to be common in glacial refugia, where range expansions and contractions can lead to cycles...
Article
Full-text available
Species of Rheum have high medicinal value, with the center of diversity in the Qinghai-Tibet Plateau (QTP) and adjacent regions. However, phylogenetic relationships of Rheum are still unclear due to fragment markers providing insufficient informative loci. Here, we sequenced and annotated plastomes of nine Rheum species, and compared the genome st...
Article
Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. How...
Article
The Sino-Himalaya region is located in the southeast margin of the Qinghai-Tibetan Plateau (QTP) with several Asian rivers in this area, namely the Yarlung Zangbo River (YZR), Salween, Mekong, and Jinshajiang River and their tributaries. All these rivers currently flow independently into the Indian Ocean, the South China Sea (Pacific Ocean) and the...
Article
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Understanding how species adapt to extreme environments is an extension of the main goals of evolutionary biology. While alpine plants are an ideal system for investigating the genetic basis of high-altitude adaptation, genomic resources in these species are still limited. In the present study, we generated reference-level transcriptomic data of fi...
Article
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Understanding the pattern of species extinction risk is key to biodiversity conservation. Previous studies showed extinction risk correlates strongly with taxon species richness. However, there is no consistent conclusion to this hypothesis, and patterns differ among different taxonomic groups. Here, we collated lists of vascular plant and terrestr...
Article
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Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved...
Preprint
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Disjunctive distribution patterns and drivers of the Sino-Japanese flora in East Asia have attracted much attention in the past decades, which is also served as an important glacial sanctuary during the quaternary glacial period. However, few studies have focused on the phylogeography, diversification and evolution of morphological character at the...
Article
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Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex ch...
Article
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The flora of northern China forms the main part of the Sino- Japanese floristic re-gion and is located in a south– north vegetative transect in East Asia. Phylogeographic studies have demonstrated that an arid belt in this region has promoted divergence of plants in East Asia. However, little is known about how plants that are restricted to the ari...
Article
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Background Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales a...
Preprint
Full-text available
Background and Aims Abelia (Caprifoliaceae) is a small genus with five species (including one artificial hybrid). The genus has a disjunct distribution across mainland China, Taiwan and the Ryukyu Islands, providing a model system to explore species dispersal mechanisms of the East Asian flora. However, the current phylogenetic relationships within...
Article
Full-text available
Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites-a wild tomato species found in diverse Andean habitats in Ecuador and Per...
Article
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Despite the well‐known biogeographic pattern in the Northern Hemisphere of disjunct distributions in plants between eastern Asia and North America, many details regarding the evolution of the disjunction between lineages of tropical Asia and tropical America remain poorly understood. Berchemia (Rhamnaceae), comprising ca. 32 species, is distributed...
Preprint
Full-text available
Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Tran...
Preprint
Full-text available
The Qinghai-Tibet Plateau (QTP) encompasses areas with a remarkably high degree of biodiversity, harboring exceptional species-rich radiations. How these radiations formed by interacting with geology, climate and ecology remains seldom examined. We investigate the roles of abiotic (environmental) and biotic (species-intrinsic) factors in driving r...
Article
Washingtonia is a genus of palms currently composed of two species, W. filifera and W. robusta, distributed in the States of Baja California, Baja California Sur, and Sonora in Mexico, and Southern California and Arizona in the United States. The group has been a taxonomic challenge due to a lack of type specimens, incomplete protologues, highly va...
Article
Washingtonia is a genus of palms currently composed of two species, W. filifera and W. robusta, distributed in the States of Baja California, Baja California Sur, and Sonora in Mexico, and Southern California and Arizona in the United States. The group has been a taxonomic challenge due to a lack of type specimens, incomplete protologues, highly va...
Article
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Xylosma longifolia is a tree species within Salicaceae and is distributed in Guizhou, Yunnan, Fujian, Guangxi, Guangdong, and Hainan provinces of China as well as in Vietnam, Laos, and India. There are no studies utilizing the complete plastome of Xylosma longifolia in the current literature. Therefore, this report provides a reference for the plas...
Preprint
Species delimitation is a difficult task in traditional morphology-based taxonomy. The ultra-barcoding approach, which uses whole plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions as extended DNA barcodes for species identification and delimitation, has been recommended as one of the candidate techniques for plant barcoding 2.0....
Article
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Background and Aims Cephalotaxus is a paleo-endemic genus in East Asia that consists of ~7–9 conifer species. Despite its great economic and ecological importance, the relationships between Cephalotaxus and related genera, as well as the interspecific relationships within Cephalotaxus, have long been controversial, resulting in contrasting taxonomi...
Article
Full-text available
Floral organ size, especially the size of the corolla, plays an important role in plant reproduction by facilitating pollination efficiency. Previous studies have outlined a hypothesized organ size pathway. However, the expression and function of many of the genes in the pathway have only been investigated in model diploid species; therefore, it is...
Preprint
Full-text available
The large number of species on our planet arises from the phenotypic variation and reproductive isolation occurring at the population level. In this study, we sought to understand the origins of such population-level variation in defensive acylsugar chemistry and mating systems in Solanum habrochaites – a wild tomato species found in diverse Andean...
Article
Full-text available
The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Ne...
Preprint
Full-text available
Background: The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax is monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the LSC. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and C...
Preprint
Full-text available
Background: The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the Large Single-Copy (LSC) region. Halesia and Pterostyrax are not supported...
Article
Full-text available
Background: Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreov...
Preprint
Full-text available
Sex chromosomes occur in diverse organisms, but their structural complexity has often prevented evolutionary analyses. Here we use two chromosome-scale reference genomes of the moss Ceratodon purpureus to trace the evolution of the sex chromosomes in bryophytes. Comparative analyses show the moss genome comprises seven remarkably stable ancestral c...
Article
Full-text available
Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the...
Article
Full-text available
Most species of Santalales (the sandalwood order) are hemiparasites, including both facultative and obligate hemiparasites. Despite its rich diversity, only a small fraction of the species in the sandalwood order have sequenced plastomes. The evolution of parasitism–associated plastome reduction in Santalales remains under-studied. Here, we report...
Article
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To evaluate phylogenetic patterns of the distribution and evolution of plant secondary metabolites (PSMs), we selected 8 classes of PSMs and mapped them onto an updated phylogenetic tree including 437 families of seed plants. Significant phylogenetic signal was detected in 17 of the 18 tested seed plant clades for at least one of the 8 PSM classes...
Article
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Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic v...
Article
Full-text available
Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionary long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in...
Preprint
Full-text available
Background Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood (ML) inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Mo...
Article
Full-text available
Abstract: Dolomiaea is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomia...
Chapter
Nicotiana tabacum L accessions vary in flower color from light pink to magenta. The differences in flower color are attributable to differences in anthocyanin content. To determine the genetic basis of flower color differences, we generated transcriptomes and quantified transcript levels of flavonoid biosynthetic genes in four N. tabacum accessions...
Article
Throughout the evolution of the angiosperm flower, developmental innovations have enabled the modification or elaboration of novel floral organs enabling subsequent diversification and expansion into new niches, for example the formation of novel pollinator relationships. One such developmental innovation is the fusion of various floral organs (syn...
Article
Highlight As a key developmental innovation leading to diversification in floral form, the fusion of floral parts is considered critically as an integration of pattern and process. Abstract Throughout the evolution of the angiosperm flower, developmental innovations have enabled the modification or elaboration of novel floral organs enabling subseq...
Preprint
Full-text available
Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic v...
Preprint
Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionary long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) and investigated the evolutionary history of K. uniflora,...
Article
Full-text available
In this study we aimed to delimit the boundaries of the Sibbaldia procumbens species complex, integrating morphological, geographical