Saša Stefanović

University of Toronto, Toronto, Ontario, Canada

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Publications (33)61.24 Total impact

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    Mihai Costea · Miguel A. García · Kurtis Baute · Saša Stefanović

    Full-text · Dataset · Jan 2016
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    Mihai Costea · Miguel A. García · Kurtis Baute · Saša Stefanović
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    ABSTRACT: The distribution of Cuscuta subg. Grammica sect. Cleistogrammica (Cuscuta pentagona clade) is centered in North America (C. campestris, C. glabrior, C. harperi, C. pentagona, C. obtusiflora, C. plattensis, C. polygonorum, C. runyonii); however, long-distance dispersal was documented to Hawaii (C. sandwichiana), South America (C. gymnocarpa, C. stenolepis, and in part C. obtusiflora), Africa (C. bifurcata, C. schlechteri), Eurasia, and Australia (C. australis). Hybrid speciation has already been documented for some members of sect. Cleistogrammica (C. sandwichiana, C. bifurcata) but previous studies strongly suggested that the extent of reticulate evolution is underestimated in Cuscuta generally, and in this section in particular. Sequence data from the nuclear internal transcribed spacer (ITS) and the plastid trnL-F region were used to reconstruct the phylogeny and gain a better understanding of the evolutionary history within the clade. Additionally, a morphometric analysis was conducted to test the phenetic distinctiveness of a select number of species with taxonomic problems: C. campestris, C. glabrior, C. gymnocarpa, and C. pentagona. Discordances between phylogenies derived from plastid and nuclear data showed that C. campestris is a hybrid, likely involving the C. runyonii/glabrior lineage as a maternal progenitor and an undiscovered species as a paternal progenitor. This latter species, an extinct or unsampled lineage, was itself inferred to be a hybrid between C. pentagona/harperi and C. australis/obtusiflora/polygonorum lineages. Both the evolutionary and morphometric results clearly showed that C. campestris is a distinct species and the negative consequences of its amalgamation with C. pentagona during the last decades are discussed. Cuscuta gymnocarpa, an enigmatic species described from specimens collected by Darwin from the Galapagos, was inferred as conspecific with C. campestris and proposed as a variety of the latter. Because C. gymnocarpa is only a form of C. campestris, the possible means of dispersal of the latter species to the Galapagos are discussed. Cuscuta modesta, a new species discovered while studying the systematics of the clade, is described and illustrated.
    Full-text · Article · Dec 2015 · Taxon
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    Mihai Costea · Miguel A. García · Kurtis Baute · Saša Stefanović

    Full-text · Article · Dec 2015 · Taxon
  • Anuar Rodrigues · Saša Stefanović

    No preview · Article · Dec 2015 · International Journal of Plant Sciences
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    ABSTRACT: DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa, and psbA-trnH and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology. In part, this is because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution, and in part because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the three plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization, and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication of hawthorn materials in Natural Health Products. Published by Oxford University Press on behalf of the Annals of Botany Company.
    Preview · Article · Apr 2015 · AoB PLANTS
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    Mihai Costea · Miguel A. García · Saša Stefanović
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    ABSTRACT: Abstract— Cuscuta (dodders, Convolvulaceae) is one of the largest and most economically important lineages of parasitic plants. The genus has a sub-cosmopolitan distribution with more than 75% of the species diversifying in the New World. The last monograph, published by Truman George Yuncker in 1932, provided a solid species-level taxonomic foundation. However, as revealed by recent phylogenetic studies, its infrageneric classification has been in great need of a taxonomic reappraisal, mainly because the morphological characters used in the previous classifications have been greatly affected by convergent evolution. Several recent phylogenetic and character evolution studies with broad sampling, as well as species-level revisions, have illustrated the deficiencies of previous classifications and provided an explicit and robust phylogenetic framework. Here we propose a new phylogenetic classification that places all 194 currently accepted species of Cuscuta into four subgenera and 18 sections. Sections have a strong morphological and biogeographical predictive value and include from one to 31 species. Thirteen section names are new or applied for the first time at the sectional rank: Babylonicae (Yunck.) M. A. García, Subulatae (Engelm.) Costea & Stefanović, Obtusilobae (Engelm.) Costea & Stefanović, Prismaticae (Yunck.) Costea & Stefanović, Ceratophorae (Yunck.) Costea & Stefanović, Umbellatae (Yunck.) Costea & Stefanović, Gracillimae Costea & Stefanović, Californicae (Yunck.) Costea & Stefanović, Indecorae (Yunck.) Costea & Stefanović, Oxycarpae (Engelm. ex Yunck.) Costea & Stefanović, Racemosae (Yunck.) Costea & Stefanović, Partitae Costea & Stefanović, and Denticulatae (Yunck.) Costea & Stefanović. An identification key to sections is included together with an overview of morphology, geographical distribution, taxonomic notes, and lists of included species.
    Full-text · Article · Feb 2015 · Systematic Botany
  • Jennifer M. Coughlan · Saša Stefanović · Timothy A. Dickinson
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    ABSTRACT: AimAsexual organisms frequently have larger ranges than their sexual progenitors, a phenomenon referred to as geographical parthenogenesis (GP). In plants, GP is associated not only with asexuality (apomixis), but also with polyploidization and hybridity (allopolyploidy). Dispersal is thought to play a role in range-size differences in other taxa, but has not been directly related to GP. Here, we compare resource allocation to dispersal-related traits in sexual diploids, asexual autopolyploids and asexual allopolyploids, and relate these differences to patterns of GP.LocationThe Pacific Northwest, North America.Methods We created distribution maps for all cytotypes known in Crataegus series Douglasianae using herbarium records. To quantify dispersal ability, we collected fruit samples from sexual diploids, apomictic allopolyploids and apomictic autopolyploids across their ranges, and used the masses of each fruit component as a proportion of the total fruit mass to gauge relative investment in dispersal and competitive ability.ResultsThe largest ranges belong to apomictic allopolyploids, whereas apomictic autotriploids and sexual diploids have the smallest ranges. Compared to sexual diploids and apomictic autotriploids, the allotetraploids exhibit a more dispersal-orientated strategy, with proportionally heavier pyrenes and more fruit pulp, but proportionally lighter seeds. Allotriploid taxa, which arose via back-crosses between sexual diploids and asexual allotetraploids, exhibit an intermediate range size as well as intermediate investment in dispersal.Main conclusionsIn Crataegus series Douglasianae, GP is associated only with allopolyploids, highlighting the potential role of hybridization in range expansion. The data suggest that allopolyploids are associated with increased resource allocation to dispersal-related traits, whereas sexual diploid C. suksdorfii and asexual autotriploid C. gaylussacia exhibit a more competition-orientated strategy. These findings are consistent with the hypothesis that hybridization contributes to patterns of GP in asexual allopolyploids, potentially by increasing their dispersal ability.
    No preview · Article · Apr 2014 · Journal of Biogeography
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    Miguel A García · Mihai Costea · Maria Kuzmina · Saša Stefanović
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    ABSTRACT: The parasitic genus Cuscuta, containing some 200 species circumscribed traditionally in three subgenera, is nearly cosmopolitan, occurring in a wide range of habitats and hosts. Previous molecular studies, on subgenera Grammica and Cuscuta, delimited major clades within these groups. However, the sequences used were unalignable among subgenera, preventing the phylogenetic comparison across the genus. We conducted a broad phylogenetic study using rbcL and nrLSU sequences covering the morphological, physiological, and geographical diversity of Cuscuta. We used parsimony methods to reconstruct ancestral states for taxonomically important characters. Biogeographical inferences were obtained using statistical and Bayesian approaches. Four well-supported major clades are resolved. Two of them correspond to subgenera Monogynella and Grammica. Subgenus Cuscuta is paraphyletic, with section Pachystigma sister to subgenus Grammica. Previously described cases of strongly supported discordance between plastid and nuclear phylogenies, interpreted as reticulation events, are confirmed here and three new cases are detected. Dehiscent fruits and globose stigmas are inferred as ancestral character states, whereas the ancestral style number is ambiguous. Biogeographical reconstructions suggest an Old World origin for the genus and subsequent spread to the Americas as a consequence of one long-distance dispersal. Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.
    Full-text · Article · Mar 2014 · American Journal of Botany
  • Anuar Rodrigues · Shana Shaya · Timothy A. Dickinson · Saša Stefanović
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    ABSTRACT: Abstract— Members of the small genus Conopholis are perennial holoparasites. They are found growing in eastern and southwestern North America and in Central America, where they attach to the roots of their oak hosts. Two species were recognized in the last taxonomic revision of the group based on geographic range and differences in floral, capsule, and bract morphology. Due to the overlapping nature of the characters used to distinguish between taxa, no single morphological feature can be relied on to differentiate between the species. A recent molecular phylogenetic study of the genus recovered three well-supported lineages, none of which corresponds entirely to the current subdivision of the genus into two species. We undertook a fine-scale morphometric study of the genus, emphasizing calyx and bract morphology. Unweighted pair-group method using arithmetic averages and principal coordinate analyses corroborate molecular data and strongly support the distinction of three separate lineages within Conopholis. A taxonomic re-alignment is proposed for the genus including three species, C. americana, C. panamensis, and C. alpina, each with various degrees of overlap with previously described taxa.
    No preview · Article · Sep 2013 · Systematic Botany
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    ABSTRACT: The Campanula pyramidalis complex is a group of closely related taxa with a distribution across the Balkans, from the Gulf of Trieste in the north to the Peloponnese Peninsula in the south, with small disjunct parts of the range in the south Apennines. Although 21 taxa were described within this complex, only three, C. pyramidalis, C. versicolor, and C. secundiflora, have been generally accepted in recent synoptical taxonomic treatments. Our molecular phylogenetic analyses based on sequences of three non-coding chloroplast regions (psbA-trnH, psbZ-trnfM, trnG-trnS) as well as of nuclear ribosomal internal transcribed spacers (nrITS), lend strong support to the recognition of several lineages which only partially correspond to generally accepted taxonomic concepts. Molecular data presented in this study showed that C. pyramidalis is a polyphyletic assemblage that segregates into three distinct lineages, one of which is described here as a new species, C. austroadriatica sp. nov. The lectotype of C. pyramidalis, redefined in a strict sense, is designated. Neither C. versicolor nor C. secundiflora were found to be strictly monophyletic, but their monophyly could not be rejected. Morphological and biogeographical implications are discussed.
    Full-text · Article · Jun 2013 · Taxon
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    Thomas Braukmann · Saša Stefanović
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    ABSTRACT: Unlike parasitic plants, which are linked to their hosts directly through haustoria, mycoheterotrophic (MHT) plants derive all or part of their water and nutrients from autothrophs via fungal mycorrhizal intermediaries. Ericaceae, the heather family, are a large and diverse group of plants known to form elaborate symbiotic relationships with mycorrhizal fungi. Using PHYA sequence data, we first investigated relationships among mycoheterotrophic Ericaceae and their close autotrophic relatives. Phylogenetic results suggest a minimum of two independent origins of MHT within this family. Additionally, a comparative investigation of plastid genomes (plastomes) grounded within this phylogenetic framework was conducted using a slot-blot Southern hybridization approach. This survey encompassed numerous lineages of Ericaceae with different life histories and trophic levels, including multiple representatives from mixotrophic Pyroleae and fully heterotrophic Monotropeae and Pterosporeae. Fifty-four probes derived from all categories of protein coding genes typically found within the plastomes of flowering plants were used. Our results indicate that the holo-mycoheterotrophic Ericaceae exhibit extensive loss of genes relating to photosynthetic function and expression of the plastome but retain genes with possible functions outside photosynthesis. Mixotrophic taxa tend to retain most genes relating to photosynthetic functions but are varied regarding the plastid ndh gene content. This investigation extends previous inferences that the loss of the NDH complex occurs prior to becoming holo-heterotrophic and it shows that the pattern of gene losses among mycoheterotrophic Ericaceae is similar to that of haustorial parasites. Additionally, we identify the most desirable candidate species for entire plastome sequencing.
    Preview · Article · Mar 2012 · Plant Molecular Biology
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    Mihai Costea · Ignacio García Ruiz · Saša Stefanović
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    ABSTRACT: The Cuscuta chapalana complex (Convolvulaceae) is a recently circumscribed clade within the subgenus Grammica that includes several little-known species from Mexico and Central and northern South America characterized by the presence of peculiar subapical multicelullar appendages on the corolla and often on the calyx lobes. Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL–F region and the 26S rDNA and internal transcribed spacer nuclear regions were used to investigate the phylogenetic relationships within the group and to test the species limits. Multicellular appendages are horn-like or tubular in shape and bear one or more stomata at their tips; hence the vernacular name “horned” dodders. Eight lineages were reconstructed; two of them, both from Mexico, were described as new species: Cuscuta bonafortunae Costea & I. García, sp. nov., and Cuscuta carnosa Costea & Stefanović, sp. nov. Cuscuta pringlei is redefined as a variety of Cuscuta strobilacea. A taxonomic treatment with an identification key, descriptions, and illustrations is provided.
    Full-text · Article · Nov 2011 · Botany
  • Mihai Costea · Ian Spence · Saša Stefanović
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    ABSTRACT: Cuscuta chinensis species complex is a small clade from subgenus Grammica (Cuscuta, Convolvulaceae). Many species of this clade exhibit crest- or dome-like multicellular appendages with stomata on the midvein/carena of calyx lobes. Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL-F region and the nuclear internal transcribed spacer (ITS) were used to investigate the phylogenetic relationships within the group and test the species limits. Based on their morphological and molecular similarly, C. chinensis and C. applanata represent one single species, and the latter was retained as a variety of the former. While the clade is centered in the southern USA and Mexico, C. chinensis var. chinensis has a disjunct distribution in Australia and Asia, which is likely the result of relatively recent long-distance dispersal. Cuscuta alata from Mexico, previously considered synonymous to C. applanata, was found to be a distinct species based on both molecular and morphological evidence. Cuscuta potosina var. potosina and var. globifera segregate into two different subclades of the C. chinensis species complex. Because these two taxa are also different morphologically, var. globifera is described as a new species, C. azteca. Cuscuta campestris, an almost cosmopolitan weed species from another clade (“Clade B”; “C. pentagona complex”), is commonly misidentified in Asia as C. chinensis, which raises questions about the identity of the Cuscuta plants used in widely commercialized medicinal herbal mixtures. A taxonomic treatment with an identification key, descriptions, and illustrations is provided.
    No preview · Article · Nov 2011 · Organisms Diversity & Evolution
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    ABSTRACT: Tests of alternative tree topologies. Results of Shimodaira-Hasegawa Tests for comparisons of alternative phylogenetic hypotheses.
    Preview · Dataset · Dec 2010
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    ABSTRACT: Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests that transferred genes may be evolutionarily important in generating mitochondrial genetic diversity. Finally, the complex relationships within each lineage of transferred genes imply a surprisingly complicated history of these genes in Plantago subsequent to their acquisition via HGT and this history probably involves some combination of additional transfers (including intracellular transfer), gene duplication, differential loss and mutation-rate variation. Unravelling this history will probably require sequencing multiple mitochondrial and nuclear genomes from Plantago. See Commentary: http://www.biomedcentral.com/1741-7007/8/147.
    Full-text · Article · Dec 2010 · BMC Biology
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    ABSTRACT: Alignments. Nucleotide sequence alignments for atp1, atp6 and matR for selected taxa.
    Preview · Dataset · Dec 2010
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    ABSTRACT: Sources of material. Sources, type of material, and voucher information for Plantago species used in this study.
    Preview · Dataset · Dec 2010
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    ABSTRACT: Additional phylogenetic analyses. The atp1, atp6 and matR data sets were re-evaluated in several alternative ways.
    Preview · Dataset · Dec 2010
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    ABSTRACT: GenBank accession numbers. Accessions are provided for all newly generated as well as previously available sequences used in this study.
    Preview · Dataset · Dec 2010
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    Eugenia Y Y Lo · Saša Stefanović · Timothy A Dickinson
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    ABSTRACT: Polyploidy plays a prominent role in the speciation process in plants. Many species are known to be part of agamic complexes comprising sexual diploids and more or less exclusively asexual polyploids. However, polyploid formation has been studied in very few cases, primarily because of the challenges in examining these cases phylogenetically. In this study, we demonstrate the use of a variety of phylogenetic approaches to unravel origins and infer reticulation history in a diploid-polyploid complex of black-fruited Crataegus. The tree approaches are shown to be useful in testing alternative hypotheses and in revealing genealogies of nuclear genes, particularly in polyploid organisms that may contain multiple copies. Compared to trees, network approaches provide a better indication of reticulate relationships among recently diverged taxa. Taken together, our data point to both the autopolyploid and allopolyploid origins of triploids in natural populations of Crataegus suksdorfii, whereas tetraploids are formed via a triploid bridge, involving the backcross of allotriploid offspring with their diploid C. suksdorfii parent, followed by gene introgression from sympatric C. douglasii. Our findings provide empirical evidence for different pathways of polyploid formation that are all likely to occur within natural populations and the allopatric establishment of neopolyploids subsequent to their formation.
    Full-text · Article · Dec 2010 · Evolution

Publication Stats

371 Citations
61.24 Total Impact Points

Institutions

  • 2008-2015
    • University of Toronto
      Toronto, Ontario, Canada
  • 2010
    • Indiana University Bloomington
      • Department of Biology
      Bloomington, Indiana, United States
  • 2009
    • University of Washington Seattle
      Seattle, Washington, United States