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A multilocus phylogeny of the world Sycoecinae fig wasps (Chalcidoidea: Pteromalidae).

Cruaud A, Underhill JG, Huguin M, Genson G, Jabbour-Zahab R, Tolley KA, Rasplus JY, van Noort S - PLoS ONE (2013)

Bottom Line: We therefore proposed a new classification for the subfamily.Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history.Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR1062 CBGP Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France.

ABSTRACT
The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades. All topologies estimated using maximum likelihood and Bayesian methods were similar and well resolved but did not support the existing classification. A high degree of morphological convergence was highlighted and several species appeared best described as species complexes. We therefore proposed a new classification for the subfamily. Our analyses revealed several cases of probable speciation on the same host trees (up to 8 closely related species on one single tree of F. sumatrana), which raises the question of how resource partitioning occurs to avoid competitive exclusion. Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history. Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.

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Phylogram of relationships among the Sycoecinae obtained from the analysis of the ClustalW alignment (combined dataset, without Gblocks cleaning, 5 partitions: mtDNA, EF-1α, ITS2, RpL27a, magonashi).Uppercase letters refer to clades discussed in the text. The new classification is indicated by colored bars on the right (yellow = oriental species, blue = afrotropical species). Nodes with likelihood bootstrap values < 70 have been collapsed. BP (> 70) and Bayesian posterior probabilities (> 0.90) are indicated at nodes. Illustrations of female habitus for the main clades are provided on the right. Host fig tree subsections are indicated between parentheses. Black boxes at nodes show cases of probable speciation on a single host Ficus species.
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pone-0079291-g002: Phylogram of relationships among the Sycoecinae obtained from the analysis of the ClustalW alignment (combined dataset, without Gblocks cleaning, 5 partitions: mtDNA, EF-1α, ITS2, RpL27a, magonashi).Uppercase letters refer to clades discussed in the text. The new classification is indicated by colored bars on the right (yellow = oriental species, blue = afrotropical species). Nodes with likelihood bootstrap values < 70 have been collapsed. BP (> 70) and Bayesian posterior probabilities (> 0.90) are indicated at nodes. Illustrations of female habitus for the main clades are provided on the right. Host fig tree subsections are indicated between parentheses. Black boxes at nodes show cases of probable speciation on a single host Ficus species.

Mentions: Phylogenetic trees of the six combined datasets were estimated using maximum likelihood (ML) and Bayesian methods. All analyses were conducted on a 150 cores Linux Cluster at CBGP as well as on the CIPRES Science Gateway [52]. Two alternative partitioning strategies were compared using Bayes factors (BF) [53]: Scheme 1: mitochondrial genes, EF-1α, ITS2, RpL27a and mago nashi versusScheme 2: first + second codon positions of mitochondrial genes, third codon positions of mitochondrial genes, EF-1α, ITS2, RpL27a and mago nashi. Following Kass and Raftery [53], Pagel and Meade [54], and Schulte and de Queiroz [55], Bayes factors were calculated using the following formula: BF = 2*(ln L1 - ln L0) + (P1-P0) * ln (0.01) where ln Li and Pi are respectively, the harmonic mean of the ln likelihoods and the number of free parameters of model i. BF values from 2 to 6 were considered positive evidence, from 6 to 10 as strong evidence, and > 10 as very strong evidence favouring the alternative hypothesis over the hypothesis. Best fitting model for each partition was identified using the Akaike information criterion [56] as implemented in MrAIC.pl 1.4.3 [57]. We performed ML analyses and associated bootstrapping using the MPI-parallelized RAxML 7.2.8-ALPHA [58]. GTRCAT approximation of models was used for ML boostrapping [58] (1000 replicates). Bootstrap percentage (BP) > 95% was considered as strong support and a BP < 70% as weak.


A multilocus phylogeny of the world Sycoecinae fig wasps (Chalcidoidea: Pteromalidae).

Cruaud A, Underhill JG, Huguin M, Genson G, Jabbour-Zahab R, Tolley KA, Rasplus JY, van Noort S - PLoS ONE (2013)

Phylogram of relationships among the Sycoecinae obtained from the analysis of the ClustalW alignment (combined dataset, without Gblocks cleaning, 5 partitions: mtDNA, EF-1α, ITS2, RpL27a, magonashi).Uppercase letters refer to clades discussed in the text. The new classification is indicated by colored bars on the right (yellow = oriental species, blue = afrotropical species). Nodes with likelihood bootstrap values < 70 have been collapsed. BP (> 70) and Bayesian posterior probabilities (> 0.90) are indicated at nodes. Illustrations of female habitus for the main clades are provided on the right. Host fig tree subsections are indicated between parentheses. Black boxes at nodes show cases of probable speciation on a single host Ficus species.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3818460&req=5

pone-0079291-g002: Phylogram of relationships among the Sycoecinae obtained from the analysis of the ClustalW alignment (combined dataset, without Gblocks cleaning, 5 partitions: mtDNA, EF-1α, ITS2, RpL27a, magonashi).Uppercase letters refer to clades discussed in the text. The new classification is indicated by colored bars on the right (yellow = oriental species, blue = afrotropical species). Nodes with likelihood bootstrap values < 70 have been collapsed. BP (> 70) and Bayesian posterior probabilities (> 0.90) are indicated at nodes. Illustrations of female habitus for the main clades are provided on the right. Host fig tree subsections are indicated between parentheses. Black boxes at nodes show cases of probable speciation on a single host Ficus species.
Mentions: Phylogenetic trees of the six combined datasets were estimated using maximum likelihood (ML) and Bayesian methods. All analyses were conducted on a 150 cores Linux Cluster at CBGP as well as on the CIPRES Science Gateway [52]. Two alternative partitioning strategies were compared using Bayes factors (BF) [53]: Scheme 1: mitochondrial genes, EF-1α, ITS2, RpL27a and mago nashi versusScheme 2: first + second codon positions of mitochondrial genes, third codon positions of mitochondrial genes, EF-1α, ITS2, RpL27a and mago nashi. Following Kass and Raftery [53], Pagel and Meade [54], and Schulte and de Queiroz [55], Bayes factors were calculated using the following formula: BF = 2*(ln L1 - ln L0) + (P1-P0) * ln (0.01) where ln Li and Pi are respectively, the harmonic mean of the ln likelihoods and the number of free parameters of model i. BF values from 2 to 6 were considered positive evidence, from 6 to 10 as strong evidence, and > 10 as very strong evidence favouring the alternative hypothesis over the hypothesis. Best fitting model for each partition was identified using the Akaike information criterion [56] as implemented in MrAIC.pl 1.4.3 [57]. We performed ML analyses and associated bootstrapping using the MPI-parallelized RAxML 7.2.8-ALPHA [58]. GTRCAT approximation of models was used for ML boostrapping [58] (1000 replicates). Bootstrap percentage (BP) > 95% was considered as strong support and a BP < 70% as weak.

Bottom Line: We therefore proposed a new classification for the subfamily.Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history.Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR1062 CBGP Centre de Biologie pour la Gestion des Populations, Montferrier-sur-Lez, France.

ABSTRACT
The Sycoecinae is one of five chalcid subfamilies of fig wasps that are mostly dependent on Ficus inflorescences for reproduction. Here, we analysed two mitochondrial (COI, Cytb) and four nuclear genes (ITS2, EF-1α, RpL27a, mago nashi) from a worldwide sample of 56 sycoecine species. Various alignment and partitioning strategies were used to test the stability of major clades. All topologies estimated using maximum likelihood and Bayesian methods were similar and well resolved but did not support the existing classification. A high degree of morphological convergence was highlighted and several species appeared best described as species complexes. We therefore proposed a new classification for the subfamily. Our analyses revealed several cases of probable speciation on the same host trees (up to 8 closely related species on one single tree of F. sumatrana), which raises the question of how resource partitioning occurs to avoid competitive exclusion. Comparisons of our results with fig phylogenies showed that, despite sycoecines being internally ovipositing wasps host-switches are common incidents in their evolutionary history. Finally, by studying the evolutionary properties of the markers we used and profiling their phylogenetic informativeness, we predicted their utility for resolving phylogenetic relationships of Chalcidoidea at various taxonomic levels.

Show MeSH
Related in: MedlinePlus