Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae)

Kuppler, A.L. Mugrabi de; Du, Baoheng; Oliver, E. G. H.; León, José Luis Ponce de; Pirie, Michael D.

doi:10.1016/j.ympev.2015.04.005

Cited by 26 publications

(31 citation statements)

References 47 publications

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“…In such cases, we should abandon our "previous-generation" assumptions and adopt "next-generation" phylogenetic approaches and data. Maureira-Butler & al., 2008) and biased against reticulation (De Villiers & al., 2013;Mugrabi de Kuppler & al., 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Both high-throughput data and complex methods may be overkill for particular phylogenetic problems. With longer periods between speciation events (or high rates of extinction), coalescence-based methods may introduce uncertainty where a combined analysis of the non-conflicting data would be more powerful (Mugrabi de Kuppler & al., 2015). Particularly in species-rich groups that are difficult to collect and/or cultivate, improved resolution resulting from combining congruent data (De Queiroz & al., 1995) from Sanger sequencing might advance our understanding long before equivalent or superior NGS data becomes available.…”

Section: Discussionmentioning

confidence: 99%

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Phylogenies from concatenated data: Is the end nigh?

Pirie

2015

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Gene trees from independent molecular markers often differ. Simple data matrix concatenation cannot represent the various biologically meaningful processes that underlie these differences, and in an age of high‐throughput DNA sequencing and coalescent‐based species tree inference methods, the approach seems increasingly quaint. I argue that concatenation still has its place in our suite of approaches, but that care should be taken when deciding which data might be combined under what circumstances. I present recommendations for avoiding the worst pitfalls of the approach.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Phylogenies from concatenated data: Is the end nigh?

Pirie

2015

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“…2014) and many other groups of angiosperms (Bertrand & al., 2015;Roy & al., 2015). Discordance may be caused by a number of different processes such as stochastic coalescence of gene lineages within a species phylogeny (incomplete lineage sorting) but also selection, hybridization, horizontal gene transfer, gene duplication/extinction, recombination and phylogenetic estimation error (Reid & al., 2014;Mugrabi de Kuppler & al., 2015).…”

Section: Introductionmentioning

confidence: 99%

Hybridization and long‐distance colonization in oat‐like grasses of South and East Asia, including an amended circumscription of Helictotrichon and the description of the new genus Tzveleviochloa (Poaceae)

Wölk

Röser

2012

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The phylogenetic relationships of 31 genera of the traditional grass tribe Aveneae, with focus on Southeast Asian species of Helictotrichon, were examined using DNA sequences of the plastid matK-psbA region, nuclear ITS, the nuclear single-copy gene topoisomerase 6 (Topo6) spanning two introns and morphology. A molecular phylogenetic analysis was performed for 121 species applying maximum parsimony and Bayesian methods. Additionally we surveyed 11 Southeast Asian taxa for structural spikelet characters including lemmas, lodicules and ovaries. The phylogenetic results of the three molecular markers revealed that several Southeast Asian species traditionally accommodated in Helictotrichon are misplaced in this genus except for H. abietetorum, H. hideoi and H. leianthum. The placement of H. polyneurum and H. sumatrense in the genus Helictotrichon requires further investigation as suggested by morphological and preliminary molecular data. Due to the occurrence of different sequence types of ITS and Topo6, both nuclear DNA markers suggested an allopolyploid origin for several Southeast Asian taxa. (1) In Helictotrichon parviflorum and H. potaninii two different sequence types of Topo6 occur, closely similar to those of Trisetum and Helictotrichon, respectively. Nuclear ITS data of both species point to affinities with Trisetum and related genera but not to Helictotrichon. Both species belong to a hitherto unknown genus that is morphologically distinct from Trisetum and Helictotrichon and is named Tzveleviochloa. (2) Two copy types (A and B) of Topo6 previously identified in African Trisetopsis, a genus encompassing predominantly sub-Saharan species that traditionally had been ascribed to Helictotrichon, also occur in two Southeast Asian species, i.e., H. junghuhnii and H. virescens. In agreement with morphological data both species need to be transferred to Trisetopsis. This expands the hitherto known eastern edge of the range of Trisetopsis from the Arabian Peninsula to China. (3) Additionally, the Chinese H. altius has a copy type sequence of Topo6 similar to that of Trisetopsis but not of Helictotrichon in its genome, whereas its plastid DNA fits Helictotrichon and relatives. Along with morphological characters this supports intermediacy between Trisetopsis and Helictotrichon. Therefore H. altius is probably an intergeneric hybrid, here named ×Trisetopsotrichon altius. The taxonomically difficult genus Helictotrichon s.l. in tropical to temperate southeastern Asia becomes disassembled into Helictotrichon s.str., the new genus Tzveleviochloa, gen. nov., and the nothogenus ×Trisetopsotrichon, nothogen. nov. The following combinations are introduced: Trisetopsis aspera, comb. nov., T. junghuhnii, comb. nov., T. virescens, comb. nov., ×Trisetopsotrichon altius, comb. nov., Tzveleviochloa burmanica, comb. nov., T. parviflora, comb. nov., T. potaninii, comb. nov. Supplementary Material DNA sequence alignments are available in the Supplementary Data section of the online version of this article at

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“…For niche-and distance-based biogeographic models Schoener's D values and geographic distances scaled to probabilities (see above) were used directly as dispersal multipliers (Appendix 3). We also assessed the impact on model fit (given the best fitting model) of a number of different values for the parameter "w", which is an exponent for the dispersal multipliers (which otherwise was fixed to "1"; Appendix 3); and coding of E. arborea as European (following Mugrabi de Kuppler et al, 2015), rather than as widespread between Europe and Tropical Africa. Further details and example files for the BioGeoBEARS analyses are presented in Appendix 3.…”

Section: Methodsmentioning

confidence: 99%

“…Just 21 of the species are found in Central and Western Europe, Macaronesia, the Mediterranean and the Middle East. This species-poor assemblage nevertheless most likely represents the ancestral area of the clade (McGuire & Kron, 2005;Mugrabi de Kuppler et al, 2015;Kowalski & Fagúndez, 2017) where the oldest lineages began to diversify c. 30 Ma (Pirie et al, 2016). From around 15 Ma, a single lineage dispersed across different biomes of the Afrotemperate (sensu White, 1981): today 23 species are known from the high mountains of Tropical Africa; 51 in Southern Africa's Drakensberg Mountains; c. 41 in Madagascar and the Mascarene islands; and c. 690 in the Cape Floristic Region of South Africa (Oliver, 2012;Pirie et al, 2016).…”

Section: Introductionmentioning

confidence: 96%

Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Pirie

Kandziora

Nuerk

et al. 2018

Preprint

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The coincidence of long distance dispersal and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a “stepping stone” between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. These results highlight the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.

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Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae)

Cited by 26 publications

References 47 publications

Phylogenies from concatenated data: Is the end nigh?

Phylogenies from concatenated data: Is the end nigh?

Hybridization and long‐distance colonization in oat‐like grasses of South and East Asia, including an amended circumscription of Helictotrichon and the description of the new genus Tzveleviochloa (Poaceae)

Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

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