Tatyana Livshultz

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

BackgroundMilkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution.ResultsA 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed.ConclusionsThe results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models.

PHYLOGENY OF APOCYNOIDEAE AND THE APSA CLADE (APOCYNACEAE S.L.)1

Abstract Phylogenetic relationships were reconstructed among 59 of 77 genera of subfamily Apocynoideae and exemplars of Periplocoideae, Secamonoideae, and Asclepiadoideae (collectively the APSA clade) using sequences from four regions of the chloroplast genome (trnL intron and trnL-trnF spacer, rpl16 intron, rps16 intron, matK and 3′ half of trnK intron) and 16 morphological characters. Apocynoideae are resolved as paraphyletic. The five tribes recognized within this subfamily in the classification of Endress and Bruyns are all paraphyletic or polyphyletic. Seven major clades of Apocynoideae are identified. The first three include genera classified predominantly in tribes Wrightieae and Malouetieae sensu Endress and Bruyns and form a paraphyletic grade to a crown clade. The crown clade includes four clades of Apocynoideae genera classified in tribes Apocyneae, Mesechiteae, and Echiteae together with Periplocoideae, Secamonoideae, and Asclepiadoideae; the latter three constitute the traditional Asclepiadaceae. Asclepiadaceae are resolved as polyphyletic, although the node that precludes a paraphyletic Asclepiadaceae does not have bootstrap support. The clade of Secamonoideae–Asclepiadoideae is well supported as sister to a clade of three African Apocynoideae genera (Baissea A. DC., Motandra A. DC., and Oncinotis Benth.). There is a strong correlation between geographic distribution and phylogeny among crown clade Apocynoideae. A New World clade is composed of American genera plus the predominantly Australasian Parsonsia R. Br. and Artia Guillaumin. An Asian clade is composed of Asian, Malesian, and Australasian genera plus the north temperate Apocynum L. Trachelospermum Lem. is polyphyletic with American and Asian species nested in the New World and Asian clades, respectively. The implications of this phylogeny for the evolution of pollen aggregation and mass transfer, the traits that were used to separate Asclepiadaceae from Apocynaceae s. str., are discussed.

The Phylogenetic Affinities of Two Mysterious Monotypic Mimosoids from Southern South America

Abstract Two monotypic genera of Mimosoideae from southern South America, Mimozyganthus and Piptadeniopsis, have been particularly difficult to classify and there has been disagreement about their relationships to other legume genera. We undertook a phylogenetic study based on molecular data from the chloroplast and nucleus, and synthesized it with new data from morphology, cytology, and palynology, in order to determine where these genera belong in the mimosoid phylogenetic tree. Mimozyganthus, an enigmatic genus whose unique morphology led workers to consider it transitional between the subfamilies Mimosoideae and Caesalpinioideae, is instead nested among the higher mimosoids on the molecular tree. Careful evaluation of the characters that were considered to be caesalpinioid-like reveals that they are not identical and are independently derived. Piptadeniopsis is most closely related to Prosopidastrum, a primarily Argentinian genus with lomentiform fruits. This is in close agreement with most morphological characters, although the pollen is different in the two genera. Piptadeniopsis, Mimozyganthus, and Prosopidastrum form a monophyletic group on all molecular trees, a result consistent with vegetative and fruiting morphology, but not floral characters. Although the relationship of this group to other taxa is unresolved in the individual molecular analyses, a combined analysis of all molecular data for a subset of the taxa reveals that the three taxa are more closely related to the Leucaena group than to Prosopis. We hypothesize that the unique floral characters of Mimozyganthus may have evolved in response to pollinator selection, and a pollination study is needed to test this hypothesis.

Climate niches of milkweeds with plesiomorphic traits (Secamonoideae; Apocynaceae) and the milkweed sister group link ancient African climates and floral evolution

PREMISE OF THE STUDY Climate change that increases mortality of plants and pollinators can create mate-finding Allee effects and thus act as a strong selective force on floral morphology. Milkweeds (Secamonoideae and Asclepiadoideae; Apocynaceae) are typically small plants of seasonally dry habitats, with pollinia and high pollen-transfer efficiency. Their sister group (tribe Baisseeae and Dewevrella) is mostly comprised of giant lianas of African rainforests, with pollen in monads. Comparison of the two groups motivated a new hypothesis: milkweeds evolved in the context of African aridification and the shifting of rainforest to dry forest. Pollinia and high pollen-transfer efficiency may have been adaptations that alleviated mate-finding Allee effects generated by high mortality during droughts. We formally tested whether milkweeds have a drier climate niche by comparing milkweeds with plesiomorphic traits (Secamonoideae) and the milkweed sister group in continental Africa. METHODS We georeferenced specimens of the milkweed sister group and Secamonoideae in continental Africa, extracted 19 climatic variables from the Worldclim model, conducted factor analysis to identify correlated suites of variables, and compared the frequency distributions of the two lineages relative to each factor. KEY RESULTS The distributions of Secamonoideae and the milkweed sister group differed significantly relative to four factors, each correlated with a distinct suite of climate parameters: (1) air temperature (Secamonoideae: cooler), (2) total and (3) summer precipitation (Secamonoideae: drier), and (4) temperature seasonality and isothermality (Secamonoideae: more seasonal and less isothermal). CONCLUSIONS Secamonoideae in continental Africa inhabit drier, cooler sites than do the milkweed sister group, consistent with a shift from rainforests to dry forests in a cooling climate.

Streptoechites gen. nov., a new genus of Asian Apocynaceae

ABSTRACT The new genus Streptoechites D.J. Middleton & Livsh., gen. nov. is described and the new combination Streptoechites chinensis (Merr.) D.J.Middleton & Livsh., comb. nov. is made. Analysis of chloroplast and nuclear loci leaves uncertain its phylogenetic position within tribe Apocyneae Rchb., but Templeton and winning sites tests reject with statistical significance its inclusion in Sindechites Oliv., Epigynum Wight or Cleghornia Wight, the three genera where it has been previously classified. In contrast, the monophyly of Urceola Roxb.and Epigynum is neither supported nor rejected, making any re-circumscription of these two genera premature. A close relationship between Urceola and the monotypic genus Aganonerion Pierre ex Spire, sampled for the first time in a molecular analysis, is supported.

Evolution on the backbone: Apocynaceae phylogenomics and new perspectives on growth forms, flowers, and fruits

PREMISE OF THE STUDY We provide the largest phylogenetic analyses to date of Apocynaceae in terms of taxa and molecular data as a framework for analyzing the evolution of vegetative and reproductive traits. METHODS We produced maximum-likelihood phylogenies of Apocynaceae using 21 plastid loci sampled from 1045 species (nearly 25% of the family) and complete plastomes from 73 species. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Apocynaceae. KEY RESULTS We obtained a well-supported phylogeny of Apocynaceae, resolving poorly understood tribal and subtribal relationships (e.g., among Amsonieae and Hunterieae, within Asclepiadeae), rejecting monophyly of Melodineae and Odontadenieae, and placing previously unsampled and enigmatic taxa (e.g., Pycnobotrya). We provide new insights into the evolution of Apocynaceae, including frequent shifts between herbaceousness and woodiness, reversibility of twining, integrated evolution of the corolla and gynostegium, and ancestral baccate fruits. CONCLUSIONS Increased sampling and selection of best-fitting models of evolution provide more resolved and robust estimates of phylogeny and character evolution than obtained in previous studies. Evolutionary inferences are sensitive to choice of phylogenetic frameworks and models.

Evolution of pyrrolizidine alkaloid biosynthesis in Apocynaceae: revisiting the defence de‐escalation hypothesis

Summary Plants produce specialized metabolites for their defence. However, specialist herbivores adapt to these compounds and use them for their own benefit. Plants attacked predominantly by specialists may be under selection to reduce or eliminate production of co‐opted chemicals: the defence de‐escalation hypothesis. We studied the evolution of pyrrolizidine alkaloids (PAs) in Apocynaceae, larval host plants for PA‐adapted butterflies (Danainae, milkweed and clearwing butterflies), to test if the evolutionary pattern is consistent with de‐escalation. We used the first PA biosynthesis specific enzyme (homospermidine synthase, HSS) as tool for reconstructing PA evolution. We found hss orthologues in diverse Apocynaceae species, not all of them known to produce PAs. The phylogenetic analysis showed a monophyletic origin of the putative hss sequences early in the evolution of one Apocynaceae lineage (the APSA clade). We found an hss pseudogene in Asclepias syriaca, a species known to produce cardiac glycosides but no PAs, and four losses of an HSS amino acid motif. APSA clade species are significantly more likely to be Danainae larval host plants than expected if all Apocynaceae species were equally likely to be exploited. Our findings are consistent with PA de‐escalation as an adaptive response to specialist attack.

The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study

Abstract Background and Aims Large clades of angiosperms are often characterized by diverse interactions with pollinators, but how these pollination systems are structured phylogenetically and biogeographically is still uncertain for most families. Apocynaceae is a clade of >5300 species with a worldwide distribution. A database representing >10 % of species in the family was used to explore the diversity of pollinators and evolutionary shifts in pollination systems across major clades and regions. Methods The database was compiled from published and unpublished reports. Plants were categorized into broad pollination systems and then subdivided to include bimodal systems. These were mapped against the five major divisions of the family, and against the smaller clades. Finally, pollination systems were mapped onto a phylogenetic reconstruction that included those species for which sequence data are available, and transition rates between pollination systems were calculated. Key Results Most Apocynaceae are insect pollinated with few records of bird pollination. Almost three-quarters of species are pollinated by a single higher taxon (e.g. flies or moths); 7 % have bimodal pollination systems, whilst the remaining approx. 20 % are insect generalists. The less phenotypically specialized flowers of the Rauvolfioids are pollinated by a more restricted set of pollinators than are more complex flowers within the Apocynoids + Periplocoideae + Secamonoideae + Asclepiadoideae (APSA) clade. Certain combinations of bimodal pollination systems are more common than others. Some pollination systems are missing from particular regions, whilst others are over-represented. Conclusions Within Apocynaceae, interactions with pollinators are highly structured both phylogenetically and biogeographically. Variation in transition rates between pollination systems suggest constraints on their evolution, whereas regional differences point to environmental effects such as filtering of certain pollinators from habitats. This is the most extensive analysis of its type so far attempted and gives important insights into the diversity and evolution of pollination systems in large clades.

THE IDENTITY OF DISCHIDIA MICHOLITZII ( APOCYNACEAE , ASCLEPIADOIDEAE )

Dischidia micholitzii N.E.Br. (Apocynaceae, Asclepiadoideae), described from a cultivated plant and erroneously assumed to be from Burma, is native to the Tenimbar and Babar island groups of Maluku, Indonesia. It is closely related to Dischidia ovata Benth. from New Guinea and Australia.