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Journal ArticleDOI

Plastid and Seed Morphology Data Support a Revised Infrageneric Classification and an African Origin of the Pantropical Genus Xylopia (Annonaceae)

TL;DR: The phylogenetic results suggest an African origin for the genus Xylopia and reveal complex biogeographic patterns, likely facilitated by long-distance dispersal.
Abstract: The floristic treatment of Engler and Diels, published in 1901, provides the only infrageneric classification of the pantropical genus Xylopia (Annonaceae) Here we test and extend that classification using molecular and seed morphology characters Phylogenetic relationships were reconstructed using data from four plastid regions obtained from 44 of the approximately 165 species in the genus, recovering four well-supported major clades Seed characters were examined for these taxa, and six aril morphologies, three previously undocumented, were distinguished; we also document the presence of a sarcotesta on the seeds of many species Molecular and seed data support recognition of five sections within the genus; one, Xylopia sect Rugosperma, is proposed here as new Our phylogenetic results suggest an African origin for the genus and reveal complex biogeographic patterns, likely facilitated by long-distance dispersal
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Journal ArticleDOI
TL;DR: A revision of the 45 species of the pantropical genus Xylopia in Tropical Africa includes descriptions of six new species and a new section of the genus, which shows specializations that promote vertebrate dispersal, primarily by hornbills and monkeys.
Abstract: A revision of the 45 species of the pantropical genus Xylopia in Tropical Africa includes descriptions of six new species and a new section of the genus. The fruits and seeds of Xylopia show specializations that promote vertebrate dispersal, primarily by hornbills and monkeys. Over half of the African species have an Area of Occupancy (AOO) less than 80 km2, suggesting that they are in need of protection. African species are classified into five sections. Section Neoxylopia, with four species, is centered in the Guineo-Congolian Region and includes X. globosa sp. nov. Section Ancistropetala, with three species, occurs in the same region. Both of these sections are endemic to Africa. Section Xylopia, which extends to Madagascar and the American tropics, has only a single species in Africa, X. aethiopica. The three species of section Verdcourtia sect. nov. are restricted to the East African coast and Madagascar. The largest number of African species, (34) belong to section Stenoxylopia, in which the seeds lack the arils found in the other sections and instead have a fleshy sarcotesta. Section Stenoxylopia is divided into two informal groups, one centered in eastern and southern Africa (X. odoratissima group) and the other centered in the wetter forests of western and central Africa (X. acutiflora group). Five new species are described in section Stenoxylopia: Xylopia nilotica sp. nov. from Sudan, South Sudan, and Uganda, Xylopia calva sp. nov. from Nigeria and Cameroon, which is allied to X. phloiodora, and Xylopia monticola sp. nov. from Nigeria and Cameroon, X. piratae sp. nov. from Ivory Coast and Ghana, and X. unguiculata sp. nov. from Gabon. The latter three species are segregates of the former Xylopia acutiflora s. l. One new combination is made at the species level, X. shirensis comb. nov. Keys, descriptions, illustrations, distribution maps, and an index to numbered collections document diversity and assist with species identification. The name Unona oliveriana Baill. was found to pre-date the name Unona lepidota Oliv., requiring the combination Meiocarpidium oliverianum comb. nov. PhytoKeys 97: 1–252 (2018) doi: 10.3897/phytokeys.97.20975 http://phytokeys.pensoft.net Copyright David M. Johnson, Nancy A. Murray. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. MONOGRAPH Launched to accelerate biodiversity research A peer-reviewed open-access journal

31 citations


Cites background or methods from "Plastid and Seed Morphology Data Su..."

  • ...For example, arils are present in the two earlier-diverging clades of the genus (Stull et al. 2017) and could be energetically more costly for the plant than the sarcotestas that predominate in more recently diverging clades....

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  • ...Four species within the X. acutiflora group were included in the molecular phylogenetic analysis of the genus by Stull et al. (2017), and all fell within a strongly supported clade along with several Madagascar species....

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  • ...Three subgroups within the X. acutiflora group are worth noting, all represented in the Stull et al. (2017) molecular study....

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  • ...Xylopia odoratissima Welwitsch ex Oliver (lectotype, designated in Stull et al. 2017, p. 221)....

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  • ...Xylopia africana (Bentham) Oliver (lectotype designated in Stull et al. 2017, p. 221)....

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Journal ArticleDOI
TL;DR: It is hypothesize that long‐distance dispersal was associated with the evolution of traits related to dispersal by large‐bodied mammals and strong‐flying, ocean‐crossing birds and bats and facilitated past intercontinental long‐ distance dispersal in the custard apple family (Annonaceae).
Abstract: AIM: Long‐distance dispersal has contributed to the disjunct biogeographical distribution of rain forest plants—something that has fascinated biogeographers since Humboldt's time. However, the dispersal agent for these tropical plant lineages remains puzzling. Here, we investigate which frugivory‐related traits may have facilitated past intercontinental long‐distance dispersal in the custard apple family (Annonaceae), a major vertebrate‐dispersed tropical plant family. We hypothesize that long‐distance dispersal was associated with the evolution of traits related to dispersal by large‐bodied mammals (e.g., large, dull‐coloured, “megafaunal” fruits) and strong‐flying, ocean‐crossing birds and bats (e.g., dehiscent, moniliform or cauliflorous fruits). LOCATION: Global. TAXON: Annonaceae. METHODS: We used a fossil‐calibrated phylogenetic framework to infer the biogeographic history of 234 Annonaceae species (10%, covering nearly all genera) in relation to the evolution of 15 frugivory‐related traits, using maximum likelihood and Bayesian inferences. Furthermore, we used linear and generalized linear models and phylogenetic simulations to test whether ancestral fruit traits during intercontinental dispersal were different from those of other lineages not involved in long‐distance dispersal. RESULTS: We inferred the ancestral Annonaceae fruits to be small with a single or few small seeds and a small number of fruitlets. These fruits were most probably apocarpous, indehiscent and/or moniliform (i.e., long beads of fruitlets). Furthermore, most of the long‐distance dispersal events in Annonaceae occurred via the expanded tropical forests in the Early Cenozoic (“geodispersal”), and were significantly associated with large (c. 3 cm long), dull‐coloured fruits and short stipes. Additionally, long‐distance dispersal was also facilitated by dehiscent, moniliform and non‐cauliflorous fruits. MAIN CONCLUSIONS: We suggest that the evolution of frugivory‐related traits associated with dispersal by frugivores that frequently move across large distances and/or barriers, such as large‐bodied mammals and strong‐flying birds, has contributed to the disjunct tropical biogeographical distribution of Annonaceae, and probably of tropical rain forest plants more generally.

23 citations


Cites background from "Plastid and Seed Morphology Data Su..."

  • ...These vertebrate dispersers facilitate germination in 458 these species by removing the aril, the sarcotesta, or both (i.e. structures that inhibit 459 germination) (Stull et al., 2017)....

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Journal ArticleDOI
TL;DR: The historical biogeography of the species‐rich flowering plant genus Goniothalamus and the wider Annonaceae tribe Annoneae is investigated to evaluate hypotheses regarding the processes underlying tropical intercontinental disjunctions and floristic exchange between biodiversity hotspots in tropical Asia.
Abstract: Aim The historical biogeography of the species-rich flowering plant genus Goniothalamus (c. 130 species) and the wider Annonaceae tribe Annoneae is investigated to evaluate hypotheses regarding the processes underlying tropical intercontinental disjunctions (‘long-distance dispersal [LDD]’ versus ‘boreotropics’) and floristic exchange between biodiversity hotspots in tropical Asia. Location Tropics, tropical Asia. Methods Divergence time estimation was based on plastid DNA sequence data (c. 10 kb; 164 Annonaceae accessions, including 65 Goniothalamus species) using an uncorrelated lognormal relaxed clock model and two fossil calibrations. Likelihood ancestral range estimation was performed using dispersal-extinction-cladogenesis models with and without time-stratified dispersal constraints. Results The boreotropics model incorporating high chances for intercontinental dispersal during 68–34 Ma fitted the data significantly better than LDD models enforcing low intercontinental dispersal rates. Multiple vicariance events were identified in Annoneae including at the Annoneae crown node (57–49 Ma, Africa/S+N America), and the Disepalum-Asimina split (27–24 Ma, Asia/N America). A wide ancestral range in continental SE Asia, W and E Malesia was inferred at the Goniothalamus crown node (24–21 Ma). Several dispersal events from continental SE Asia/W Malesia were identified in the Miocene: two north-eastwards to the Philippines, one eastwards to the Sahul Shelf and two westwards to India. Main conclusions The boreotropics hypothesis provides a well-supported, plausible explanation for the disjunctions and dispersal–vicariance patterns in tribe Annoneae. The wide distribution inferred at the Goniothalamus crown node indicates that its ancestors already bridged the marine gap between the Sunda and Sahul Shelves by LDD or rafting on tectonic plate microfragments. Dispersal across long-standing water bodies in Malesia occurred multiple times from the early Miocene as marine gaps decreased following tectonic plate convergence and land emergence. Substantially older crown group divergence estimates compared with previous studies indicate that hypotheses of rapid recent radiation in Goniothalamus must be rejected.

22 citations


Additional excerpts

  • ...Plastid and seed morphology data support a revised infrageneric classification and an African origin of the Pantropical genus Xylopia (Annonaceae)....

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  • ...Taxonomy and biogeography of the New Caledonian species of Xylopia L. (Annonaceae)....

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  • ...Unit D was not further subdivided as phylogenetic data indicate that Indian and Australian species in several genera are likely derived from other Asian taxa (e.g. Artabotrys, Huberantha: Thomas et al., 2015; Meiogyne: Thomas et al., 2012b; Pseuduvaria: Su & Saunders, 2009; Uvaria: Zhou, Su, Thomas, & Saunders, 2012; Xylopia: Stull et al., 2017), and previous divergence time estimates indicate that likely none of these represent Gondwanan relictual lineages which originated in situ and rafted to Asia on the Indian or Australia fragments (e.g. Couvreur et al., 2011; Thomas et al., 2015)....

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  • ...Anaxagorea (Scharaschkin & Doyle, 2005); Guatteria (Erkens, Maas, & Couvreur, 2009); Isolona (Couvreur, Chatrou, Sosef, & Richardson, 2008); Pseuduvaria (Su & Saunders, 2009) and Xylopia (Stull et al., 2017)....

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  • ...…Thomas et al., 2015; Meiogyne: Thomas et al., 2012b; Pseuduvaria: Su & Saunders, 2009; Uvaria: Zhou, Su, Thomas, & Saunders, 2012; Xylopia: Stull et al., 2017), and previous divergence time estimates indicate that likely none of these represent Gondwanan relictual lineages which…...

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Journal ArticleDOI
TL;DR: A linear sequence of four subfamilies, 15 tribes and 106 genera of the magnoliid family Annonaceae is provided, based on state-of-the-art and stable phylogenetic relationships, which facilitates the organisation ofAnnonaceae herbarium specimens.
Abstract: This paper provides a linear sequence of four subfamilies, 15 tribes and 106 genera of the magnoliid family Annonaceae, based on state-of-the-art and stable phylogenetic relationships. The linear sequence facilitates the organisation of Annonaceae herbarium specimens.

20 citations


Additional excerpts

  • ...…into existing tribes (Chaowasku et al. 2012; Chaowasku et al. 2013; Guo et al. 2014; Xue et al. 2014; Chaowasku et al. 2015; Couvreur et al. 2015; Tang et al. 2015; Thomas et al. 2015; Ortiz-Rodriguez et al. 2016; Ghogue et al. 2017; Guo et al. 2017a; Stull et al. 2017; Pirie et al. 2018)....

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Journal ArticleDOI
TL;DR: The results suggest that the liana habit, the presence of circadian pollinator trapping, androdioecy, and the dispersal of seeds as single-seeded monocarp fragments are closely correlated with higher diversification rates; pollen aggregation and anther septation, in contrast, are associated with lower diverification rates.

19 citations

References
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Journal ArticleDOI
TL;DR: In this article, a new estimate minimum information theoretical criterion estimate (MAICE) is introduced for the purpose of statistical identification, which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure.
Abstract: The history of the development of statistical hypothesis testing in time series analysis is reviewed briefly and it is pointed out that the hypothesis testing procedure is not adequately defined as the procedure for statistical model identification. The classical maximum likelihood estimation procedure is reviewed and a new estimate minimum information theoretical criterion (AIC) estimate (MAICE) which is designed for the purpose of statistical identification is introduced. When there are several competing models the MAICE is defined by the model and the maximum likelihood estimates of the parameters which give the minimum of AIC defined by AIC = (-2)log-(maximum likelihood) + 2(number of independently adjusted parameters within the model). MAICE provides a versatile procedure for statistical model identification which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure. The practical utility of MAICE in time series analysis is demonstrated with some numerical examples.

47,133 citations


"Plastid and Seed Morphology Data Su..." refers methods in this paper

  • ...We used an Akaike information criterion (AIC) test (Akaike 1974) to select among three different transition models for the reconstruction: 1) equal rates model, 2) equal forward/reverse transition rates model, and an all-ratesdifferent (ARD) model; in all cases the ARD model was identified as the…...

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Journal ArticleDOI
TL;DR: This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
Abstract: Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting postanalyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU

23,838 citations


"Plastid and Seed Morphology Data Su..." refers methods in this paper

  • ...For the combined maximum likelihood analysis, conducted using RAxML v. 8.2.12 (Stamatakis 2014) and the GTR1G model, we implemented two model partitioning strategies: 1) by locus (i.e. model parameters were optimized for each of the four gene/spacer partitions) and 2) with a single set of model…...

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Journal ArticleDOI
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
Abstract: Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.

20,627 citations


"Plastid and Seed Morphology Data Su..." refers methods in this paper

  • ...For the Bayesian analysis of the combined data set, implemented in MrBayes v. 3.2.1 (Huelsenbeck and Ronquist 2001; Ronquist et al. 2012), we ran 10 million generations with four chains sampling the posterior distribution every 1,000 generations....

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Journal ArticleDOI
TL;DR: The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
Abstract: Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

18,718 citations


"Plastid and Seed Morphology Data Su..." refers methods in this paper

  • ...For the Bayesian analysis of the combined data set, implemented in MrBayes v. 3.2.1 (Huelsenbeck and Ronquist 2001; Ronquist et al. 2012), we ran 10 million generations with four chains sampling the posterior distribution every 1,000 generations....

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Journal ArticleDOI
TL;DR: From the kinetic data, it becomes evident that the reductive amination reaction is highly adaptive to the ammonium environment.

14,480 citations

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