J Syst Evol

08 March 2017, Volume 55 Issue 2

Cover illustration: Molecular phylogenetic and morphological investigation of Staphyleaceae revealed five major clades. The investigation for morphological synapomorphies in Staphyleaceae included examination of venation in leaf teeth, ultrastructural epicuticular wax features of leaves, and pollen. All images of leaf teeth, epicuticular waxes, and pollen are shown in relative size, respectively, and are presented in the paper and/or included in linked external sources with voucher information and scale bars. Art pl [Detail] ...

Review

Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons

Mark P. Simmons

J Syst Evol. 2017, 55(2): 85-109.
https://doi.org/10.1111/jse.12233

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Both traditional as well as 10 more recent methods of coding characters from exons of protein-coding genes are reviewed. The more recent methods collectively blur the distinction between nucleotide and amino-acid coding and enable investigators to carefully quantify the effects of different sources of phylogenetic signal as well as their potential biases. Codon models, which explicitly model silent and replacement substitutions, are a major advance and are expected to be broadly useful for simultaneously inferring recent and ancient divergences, unlike amino-acid coding. Degeneracy coding, wherein ambiguity codes are used to eliminate silent substitutions at the individual-nucleotide level, has clear advantages over scoring amino-acid characters. Nucleotide, codon, and amino-acid models are now directly comparable with easy-to-use programs, and widely used phylogenetics programs can analyze partitioned supermatrices that incorporate all three types of model. Therefore, it should become standard practice to test among these alternative model types before conducting parametric phylogenetic analyses. An earlier study of 78 protein-coding genes from 360 green-plant plastid genomes is used as an empirical example with which to quantify the relative performance of alternative character-coding methods using five quantification measures. Codon models were selected as having the best fit to the data, yet were outperformed by nucleotide models for all five quantification measures. Third-codon positions were found to be an important source of phylogenetic signal and even outperformed analyses of first and second positions for some measures. Degeneracy coding generally performed at least as well as amino-acid coding and is an arguably more effective alternative.

Research Articles

A phylogeny of the genus Encyclia (Orchidaceae: Laeliinae), with emphasis on the species of the Northern Hemisphere

Carlos L. Leopardi-Verde, Germán Carnevali, Gustavo A. Romero-González

J Syst Evol. 2017, 55(2): 110-123.
https://doi.org/10.1111/jse.12225

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Encyclia comprises over 150 species of orchids that occupy mainly seasonally dry habitats in tropical and subtropical America and are usually restricted to one or a few ecoregions. To determine whether species found in the same or neighboring ecoregions are closely related, we sampled more than 50 taxa, with an emphasis on species found in Mexico and Central America. We evaluated five DNA markers for their phylogenetic utility: the nuclear low copy gene PHYC, a plastid spacer region trnL-F, a fragment of the plastid ycf1 gene, rpl32-trnL, and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA; we sampled only the last three markers for the main analyses based on an assessment of phylogenetic informativeness. We analyzed plastid regions and ITS separately in phylogenetic inference using a variety of methods, as we found strong incongruence between them, according to the ILD test. We also estimated clade ages using a relaxed molecular clock with indirect calibrations based on a larger taxonomic sampling. Encyclia is a monophyletic genus that originated ca. 12.43 Ma (10.55–14.25 Ma) ago, and has undergone several recent evolutionary radiations. We found a strong association between phylogenetic relationships and the geographic distribution of species and clades in the Caribbean, Central American, and the Pacific coast of Megamexico. Several groups of Encyclia occur in the latter region, the most species-rich being the E. meliosma complex, which is restricted to the Pacific slope of Mexico from north of the Isthmus of Tehuantepec up to Sonora.
A molecular phylogeny of Staphyleaceae: Implications for generic delimitation and classical biogeographic disjunctions in the family

AJ Harris, Ping-Ting Chen, Xin-Wei Xu, Jian-Qiang Zhang, Xue Yang, Jun Wen

J Syst Evol. 2017, 55(2): 124-141.
https://doi.org/10.1111/jse.12236

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Staphyleaceae traditionally comprises three genera of temperate and tropical trees and shrubs: Euscaphis Siebold & Zucc., Staphylea L., and Tuprinia Vent. These genera are clearly supported by morphology, but a recent classification based on four chloroplast genes and nuclear ITS treats Staphylea, Euscaphis, and New WorldTurpinia in Staphylea s.l. and Old World Turpinia in Dalrympelea Roxb. In this study, our objectives were to (1) resolve the phylogenetic relationships within Staphyleaceae using two nuclear and six chloroplast markers, (2) explore morphological synapomorphies that support major clades, and (3) discuss the implications of our results on generic delimitation and biogeography. Our phylogenetic results show five major clades in Staphyleaceae: (1) Old World Turpinia, (2) New World Turpinia, (3) a clade of exclusively Old World Staphylea, (4) an Asian-North American clade of Staphylea comprising all New World species and the rest of the Old World ones, and (5) Euscaphis. Within the two clades each of Staphylea and Turpinia, morphological features traditionally used for delimiting the genera may exhibit convergence. Among morphological features examined in this study, we found that pollen is not taxonomically informative, features of leaf teeth and epicuticular waxes show limited support for the traditional genera of Staphylea and Tuprinia, respectively, and petal length (i.e., flower size) is significantly smaller in Old World Turpinia compared to New World Turpinia. With respect to biogeography, our results support a rare disjunction between eastern North America and the Himalayas.
Origin and evolutionary implications of introns from analysis of cellulose synthase gene

Punit Bhattachan, Bo Dong

J Syst Evol. 2017, 55(2): 142-148.
https://doi.org/10.1111/jse.12235

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Spliceosomal introns are present in diverse eukaryotic but not prokaryotic genes. However, their evolutionary origin is still arguable. Here, we address this question through an analysis of the cellulose synthase gene, which is present only in urochordate among the animal lineages due to horizontal transfer from a bacterial ancestor in the distant past. We hypothesize that this gene in urochordate contains primordial intron positions and attempted to find them by comparisons with the plant cellulose synthase gene intron positions. However, we could not find distinct conservation of intron positions; therefore, we believe that there was only random insertion of introns in the urochordate cellulose synthase gene. In addition, the protosplice site tendency to conserved phase zero intron positions in urochordates is only 54%, compared with 76% in plants. This shows independent origins of introns in the cellulose synthase gene of urochordates and plants during eukaryotic evolution. Therefore, we concluded that intron origin is a eukaryotic invention.
Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution

Dong-Yuan Song, Zhe Wang, Zhuo-Jun Song, Cheng-Chuan Zhou, Peng-Hao Xu, Jie Yang, Ji Yang, Bao-Rong Lu

J Syst Evol. 2017, 55(2): 149-157.
https://doi.org/10.1111/jse.12230

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Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice-planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy-rice specific novel single nucleotide polymorphisms (SNPs) by genome-wide comparison between DNA sequences of weedy and cultivated rice, in addition to polymerase chain reaction fingerprinting at 22 selected novel SNP loci in weedy rice populations. A great number of novel SNPs were identified across the weedy rice genome. High frequencies of the novel SNPs were determined at the 22 selected loci, although with considerable variation among weedy rice populations in different rice-planting regions. The highest frequency (∼57%) of novel SNPs was identified in weedy rice populations from Jiangsu that experienced the most dramatic changes in rice farming styles, including the shift from transplanting to direct seeding, and from indica to japonica varieties. The lowest frequency (∼29%) was detected in weedy rice populations from Northeast China, where rice farming has undergone relatively less change. The association between frequencies of novel SNPs in weedy rice populations and the extent of changes in rice farming styles suggests the critical role of adaptive mutation and accumulation of the mutation influenced by human activities in the rapid evolution of weedy rice.
Fungal diversity and specificity in Cephalanthera damasonium and C. longifolia (Orchidaceae) mycorrhizas

Lorenzo Pecoraro, Laiqiang Huang, Tancredi Caruso, Silvia Perotto, Mariangela Girlanda, Lei Cai, Zhong-Jian Liu

J Syst Evol. 2017, 55(2): 158-169.
https://doi.org/10.1111/jse.12238

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Orchids depend on mycorrhizal fungi for their nutrition, at least in the early stages of their growth and development, and in many cases throughout the life. In spite of the increasing number of studies describing fungal diversity in orchids, there is still more to be learnt about the identity of fungal partners and specificity in orchid mycorrhizal associations. We investigated the fungal communities associated with the roots of Cephalanthera damasonium (Mill.) Druce and C. longifolia (L.) Fritsch adult plants, using morphological methods and fungal internal transcribed spacer-DNA polymerase chain reaction amplification, cloning, and sequencing. A range of fungi belonging to Basidiomycota and Ascomycota was uncovered in the roots of the two investigated orchid species, showing a low degree of mycorrhizal specificity. At least 11 fungal taxa, including Cenococcum geophilum Fr., Ceratobasidium sp., Exophiala salmonis J. W. Carmich., Hymenogastraceae, and Sebacinaceae colonized C. damasonium roots, while approximately 9 fungal types, such as Bjerkandera adusta (Willd.) P. Karst., Phlebia acerina Peck, Sebacinaceae,Tetracladium sp., and Tomentella sp. associated with C. longifolia. Phylogenetic and statistical analyses indicated significant differences in the fungal communities associated with the two studied Cephalanthera species, as well as distinct mycorrhizal partners associated with each orchid plant. Our results strongly suggest that both C. damasonium and C. longifolia are generalist in their mycorrhizal associations.