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The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family’s complex infra‐familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework. Nuclear DNA sequence data were generated for 123 genera (86%) of Sapindaceae using target sequence capture with the Angiosperms353 universal probe set. HybPiper was used to produce aligned DNA matrices. Phylogenetic inferences were obtained using coalescence‐based and concatenated methods. The clades recovered are discussed in light of both benchmark studies to identify synapomorphies and distributional evidence to underpin an updated infra‐familial classification. Coalescence‐based and concatenated phylogenetic trees had identical topologies and node support, except for the placement of Melicoccus bijugatus Jacq. Twenty‐one clades were recovered, which serve as the basis for a revised infra‐familial classification. Twenty tribes are recognized in four subfamilies: two tribes in Hippocastanoideae, two in Dodonaeoideae, and 16 in Sapindoideae (no tribes are recognized in the monotypic subfamily Xanthoceratoideae). Within Sapindoideae, six new tribes are described: Blomieae Buerki & Callm.; Guindilieae Buerki, Callm. & Acev.‐Rodr.; Haplocoeleae Buerki & Callm.; Stadmanieae Buerki & Callm.; Tristiropsideae Buerki & Callm.; and Ungnadieae Buerki & Callm. This updated classification provides a backbone for further research and conservation efforts on this family.
Sven Buerki; Martin W. Callmander; Pedro Acevedo‐Rodriguez; Porter P. Lowry; Jérôme Munzinger; Paul Bailey; Olivier Maurin; Grace E. Brewer; Niroshini Epitawalage; William J. Baker; Félix Forest. An updated infra‐familial classification of Sapindaceae based on targeted enrichment data. American Journal of Botany 2021, 108, 1234 -1251.
AMA StyleSven Buerki, Martin W. Callmander, Pedro Acevedo‐Rodriguez, Porter P. Lowry, Jérôme Munzinger, Paul Bailey, Olivier Maurin, Grace E. Brewer, Niroshini Epitawalage, William J. Baker, Félix Forest. An updated infra‐familial classification of Sapindaceae based on targeted enrichment data. American Journal of Botany. 2021; 108 (7):1234-1251.
Chicago/Turabian StyleSven Buerki; Martin W. Callmander; Pedro Acevedo‐Rodriguez; Porter P. Lowry; Jérôme Munzinger; Paul Bailey; Olivier Maurin; Grace E. Brewer; Niroshini Epitawalage; William J. Baker; Félix Forest. 2021. "An updated infra‐familial classification of Sapindaceae based on targeted enrichment data." American Journal of Botany 108, no. 7: 1234-1251.
Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152–161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.
Sara E. Simmonds; James F. Smith; Christopher Davidson; Sven Buerki. Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae). Molecular Phylogenetics and Evolution 2021, 163, 107229 .
AMA StyleSara E. Simmonds, James F. Smith, Christopher Davidson, Sven Buerki. Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae). Molecular Phylogenetics and Evolution. 2021; 163 ():107229.
Chicago/Turabian StyleSara E. Simmonds; James F. Smith; Christopher Davidson; Sven Buerki. 2021. "Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)." Molecular Phylogenetics and Evolution 163, no. : 107229.
There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining tool developed specifically for G2P research. This R package uses automation to make the G2P review process efficient and unbiased, while also generating hypothesized associations between genes and phenotypes within a taxonomical framework. We applied the package to a literature review for drought-tolerance in plants. The analysis provides biologically meaningful results within the known framework of drought tolerance in plants. Overall, the package is useful for conducting literature reviews for genome to phenome projects, and also has broad appeal to scientists investigating a wide range of study systems as it can conduct analyses under the auspices of three different kingdoms (Plantae, Animalia, and Fungi).
John Wojahn; Stephanie Galla; Anthony Melton; Sven Buerki. G2PMineR: A Genome to Phenome Literature Review Approach. Genes 2021, 12, 293 .
AMA StyleJohn Wojahn, Stephanie Galla, Anthony Melton, Sven Buerki. G2PMineR: A Genome to Phenome Literature Review Approach. Genes. 2021; 12 (2):293.
Chicago/Turabian StyleJohn Wojahn; Stephanie Galla; Anthony Melton; Sven Buerki. 2021. "G2PMineR: A Genome to Phenome Literature Review Approach." Genes 12, no. 2: 293.
Although vanilla is one of the most popular flavours in the world, there is still uncertainty concerning the native distribution of the species that produces it, Vanilla planifolia. To circumscribe the native geographical extent of this economically important species more precisely, we propose a new landscape-based approach to incorporate information from open-source databases and validate occurrences. In this approach, we include metrics to account for habitat suitability and population sustainability in terms of the biotic (co-occurrence of pollinators and dispersers) and abiotic (habitat quality) factors limiting plant distributions. To further validate occurrences within the resulting distribution, we compare the presence of morphologically similar wild relatives, assess the heterogeneity of ecological niches and verify the correct identification of herbarium specimens. Results from this approach suggest that V. planifolia has a larger geographical distribution than previously recognized; we hypothesize that populations naturally dispersed from Mesoamerica and became established in South America (with a south-eastern limit in Brazil). The recognition of an improved estimate of the distribution of this species will increase the accuracy of predictive models, promote further species circumscription, improve the efficacy of conservation strategies, and help to ensure the sustainability of a valuable, sought-after spice.
Paige Ellestad; Félix Forest; Marcelo Serpe; Stephen J Novak; Sven Buerki. Harnessing large-scale biodiversity data to infer the current distribution of Vanilla planifolia (Orchidaceae). Botanical Journal of the Linnean Society 2021, 196, 407 -422.
AMA StylePaige Ellestad, Félix Forest, Marcelo Serpe, Stephen J Novak, Sven Buerki. Harnessing large-scale biodiversity data to infer the current distribution of Vanilla planifolia (Orchidaceae). Botanical Journal of the Linnean Society. 2021; 196 (3):407-422.
Chicago/Turabian StylePaige Ellestad; Félix Forest; Marcelo Serpe; Stephen J Novak; Sven Buerki. 2021. "Harnessing large-scale biodiversity data to infer the current distribution of Vanilla planifolia (Orchidaceae)." Botanical Journal of the Linnean Society 196, no. 3: 407-422.
Basin big sagebrush (Artemisia tridentata subsp. tridentata) is a keystone species of the sagebrush steppe, a widespread ecosystem of western North America threatened by climate change. The study’s goal was to develop an in vitro method of propagation for this taxon to support genome sequencing and genotype-by-environment research on drought tolerance. Such research may ultimately facilitate the reintroduction of big sagebrush in degraded habitats. Seedlings were generated from two diploid mother plants (2n = 2x = 18) collected in environments with contrasting precipitation regimes. The effects of IBA and NAA on rooting of shoot tips were tested on 45 individuals and 15 shoot tips per individual. Growth regulator and individual-seedling effects on percent rooting and roots per shoot tip were evaluated using statistical and clustering analyses. Furthermore, rooted shoot tips were transferred into new media to ascertain their continued growth in vitro. The results suggest that A. tridentata is an outbred species, as shown by individuals’ effect on rooting and growth. IBA addition was the most effective method for promoting adventitious rooting, especially in top-performing individuals. These individuals also have high survival and growth rates upon transferring to new media, making them suitable candidates for generating biomass for genome sequencing and producing clones for genotype-by-environment research.
Rachael Barron; Peggy Martinez; Marcelo Serpe; Sven Buerki. Development of an In Vitro Method of Propagation for Artemisia tridentata subsp. tridentata to Support Genome Sequencing and Genotype-by-Environment Research. Plants 2020, 9, 1717 .
AMA StyleRachael Barron, Peggy Martinez, Marcelo Serpe, Sven Buerki. Development of an In Vitro Method of Propagation for Artemisia tridentata subsp. tridentata to Support Genome Sequencing and Genotype-by-Environment Research. Plants. 2020; 9 (12):1717.
Chicago/Turabian StyleRachael Barron; Peggy Martinez; Marcelo Serpe; Sven Buerki. 2020. "Development of an In Vitro Method of Propagation for Artemisia tridentata subsp. tridentata to Support Genome Sequencing and Genotype-by-Environment Research." Plants 9, no. 12: 1717.
Pandanus odorifer (Pandanaceae) is an economically important species distributed on coasts from India and Sri Lanka to South China through tropical Asian countries. Pandanus odoratissimus has been widely used as the accepted name for the species, but P. odoratissimus is in reality a superfluous and illegitimate name. No original material of P. odorifer has been traced, and a neotype is designated here for that name.
Martin W. Callmander; Timothy J. Gallaher; John McNeill; Henk Beentje; Altafhusain B. Nadaf; David J. Middleton; Sven Buerki. Neotypification of Pandanus odorifer , the correct name for P. odoratissimus (Pandanaceae). TAXON 2020, 70, 182 -184.
AMA StyleMartin W. Callmander, Timothy J. Gallaher, John McNeill, Henk Beentje, Altafhusain B. Nadaf, David J. Middleton, Sven Buerki. Neotypification of Pandanus odorifer , the correct name for P. odoratissimus (Pandanaceae). TAXON. 2020; 70 (1):182-184.
Chicago/Turabian StyleMartin W. Callmander; Timothy J. Gallaher; John McNeill; Henk Beentje; Altafhusain B. Nadaf; David J. Middleton; Sven Buerki. 2020. "Neotypification of Pandanus odorifer , the correct name for P. odoratissimus (Pandanaceae)." TAXON 70, no. 1: 182-184.
Martin W. Callmander; Sven Buerki; Roy E. Gereau. (2772) Proposal to conserve the name Pandanus ornatus Kurz ( Benstonea ornata ) against P. ornatus W. Bull with a conserved type ( Pandanaceae ). TAXON 2020, 69, 1115 -1116.
AMA StyleMartin W. Callmander, Sven Buerki, Roy E. Gereau. (2772) Proposal to conserve the name Pandanus ornatus Kurz ( Benstonea ornata ) against P. ornatus W. Bull with a conserved type ( Pandanaceae ). TAXON. 2020; 69 (5):1115-1116.
Chicago/Turabian StyleMartin W. Callmander; Sven Buerki; Roy E. Gereau. 2020. "(2772) Proposal to conserve the name Pandanus ornatus Kurz ( Benstonea ornata ) against P. ornatus W. Bull with a conserved type ( Pandanaceae )." TAXON 69, no. 5: 1115-1116.
Premise of the Study While brinjal eggplant (Solanum melongena L.) is the second most important solanaceous fruit crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step‐wise expansion of the eggplant group from Africa to Asia. Methods We use museum collections to generate nuclear and full‐plastome data for all species of the Eggplant clade. We combine a phylogenomic approach with distribution data to infer a biogeographic scenario for the clade. Key Results The Eggplant clade has Pleistocene origins in northern Africa. Dispersals to tropical Asia gave rise to Solanum insanum, the wild progenitor of the eggplant, and to African distinct lineages of widespread and southern African species. Results suggest that spread of the species to southern Africa has been recent and likely facilitated by large mammalian herbivores, such as the African elephant and impala feeding on Solanum fruit. Conclusions Rather than a linear ‘Out Of Africa’ sequence, our results are more consistent with an initial dispersal event into Asia, and subsequent wide dispersal and differentiation across Africa driven by large mammalian herbivores. Our evolutionary results will affect future work on eggplant domestication and affect the use of wild relatives in breeding of this increasingly important solanaceous crop.
Xavier Aubriot; Sandra Knapp; Mindy M. Syfert; Péter Poczai; Sven Buerki. Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongenaL.) and its wild relatives. American Journal of Botany 2018, 105, 1175 -1187.
AMA StyleXavier Aubriot, Sandra Knapp, Mindy M. Syfert, Péter Poczai, Sven Buerki. Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongenaL.) and its wild relatives. American Journal of Botany. 2018; 105 (7):1175-1187.
Chicago/Turabian StyleXavier Aubriot; Sandra Knapp; Mindy M. Syfert; Péter Poczai; Sven Buerki. 2018. "Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongenaL.) and its wild relatives." American Journal of Botany 105, no. 7: 1175-1187.
This study reports the first description of the gastrointestinal (GIT) morphology of a lemur species (Cheirogaleus major É. Geoffroy, 1812) of the family Cheirogaleidae using a museum collection deposited at the Natural History Museum, London. Knowledge on GIT morphology is the key to assessment of the diet of animals, especially those that are highly threatened. Several studies predicted the demise of lemurs (>100 species representing 20% of the world's primate diversity) by 2080 unless the conservation community acts quickly. In this context, museum collections could provide valuable evidence on the biology of lemurs to underpin conservation protocols. The feeding ecology of the omnivorous Cheirogaleus major is poorly known due to its secretive periods of hibernation and daily torpor, nocturnal activity and solitary foraging habit. To better understand the biology of C. major, we described and compared its GIT morphology with those of six other species for which we have published data, especially the frugivore taxa (Eulemur coronatus Grey, 1842 and Varecia variegata Kerr, 1792). Our findings showed that C. major has a GIT morphology similar to those of E. coronatus and V. variegata. This is especially the case because of its caecum, which is short and only slightly sacculated suggesting that it is not suitable for microbial breakdown of plant cell wall (unlike those of Propithecus species, Lemur catta, and Hapalemur griseus). This result is in line with ecological studies suggesting that C. major obtains its protein and carbohydrate intake from fruits and to some extent arthropods and not from the digestion of leaves as previously hypothesized. In light of this new evidence, conservation programmes should account for both the lemur and its associated flora. Overall, this study demonstrates the unique potential of museum collections to study the nutritional ecology of threatened animals and their potential role in supporting conservation.
Sven Buerki; Roberto Portela Miguez. Museum collections are the key to studying lemurs’ diet: gastrointestinal morphology of Cheirogaleus major. Systematics and Biodiversity 2018, 16, 483 -487.
AMA StyleSven Buerki, Roberto Portela Miguez. Museum collections are the key to studying lemurs’ diet: gastrointestinal morphology of Cheirogaleus major. Systematics and Biodiversity. 2018; 16 (5):483-487.
Chicago/Turabian StyleSven Buerki; Roberto Portela Miguez. 2018. "Museum collections are the key to studying lemurs’ diet: gastrointestinal morphology of Cheirogaleus major." Systematics and Biodiversity 16, no. 5: 483-487.
A new species of Alectryon Gaertn. (Sapindaceae) endemic to the Fijian archipelago is described as A. vitiensis Buerki, Lowry, Munzinger & Callm. based on morphological and molecular evidence. It can easily be distinguished from the two congeners currently known from Fiji by its smaller leaves, subsessile leaflets, apetalous flowers, and crested fruits. A phylogenetic analysis using ITS sequence data shows that the new species is closely related to two Australian endemics, A. diversifolius (F. Muell.) S. T. Reynolds and A. oleifolius (Desf.) S. T. Reynolds, but differs in having compound leaves covered with a golden indument. Moreover, the Australian taxa are associated with dry habitats, whereas the new species from Fiji is confined to evergreen humid forests. Among apetalous species (all of which belong to a well-supported clade), A. vitiensis morphologically most closely resembles the generic type, A. excelsus Gaertn., endemic to New Zealand, but they differ from one another in the type of indument covering their branches and leaves and the arrangement, shape, and nature of the indument on their leaflets; and they belong to different clades. The new species is provisionally assigned a conservation status of “Endangered” according to the IUCN Red List criteria.
Sven Buerki; Porter P. Lowry; Jérôme Munzinger; Marika Tuiwawa; Alivereti Naikatini; Martin W. Callmander. Alectryon vitiensis: A New Species of Sapindaceae Endemic to Fiji. Novon, A Journal for Botanical Nomenclature 2017, 25, 421 -429.
AMA StyleSven Buerki, Porter P. Lowry, Jérôme Munzinger, Marika Tuiwawa, Alivereti Naikatini, Martin W. Callmander. Alectryon vitiensis: A New Species of Sapindaceae Endemic to Fiji. Novon, A Journal for Botanical Nomenclature. 2017; 25 (4):421-429.
Chicago/Turabian StyleSven Buerki; Porter P. Lowry; Jérôme Munzinger; Marika Tuiwawa; Alivereti Naikatini; Martin W. Callmander. 2017. "Alectryon vitiensis: A New Species of Sapindaceae Endemic to Fiji." Novon, A Journal for Botanical Nomenclature 25, no. 4: 421-429.