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52 results for “phylogenetic conflict”
Interrogating genomic data in the phylogenetic placement of treeshrews reveals potential sources of conflict
<p>The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In this study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. The results suggest that the data has statistical support for two hypotheses for the placements of treeshrews, sister to Primatomorpha and to Primatomorpha + Glires. While we observe differences in properties of loci of different types (e.g., CDS, intron, etc.) with respect to the strength of the signal, the support for any particular topology is not dependent on the properties of the data. Rather, we show that the method of phylogenetic signal assessment, as well as whether the signal is measured using the full dataset or only loci with the strongest signal, impacts the results much more.</p>
Figure 3 in RESOLVING PHYLOGENETIC AND TAXONOMIC CONFLICT IN BEGONIA
Figure 3. Differences in basal topology of Begonia phylogeny shown on diagrammatic representations of maximum likelihood analysis of chloroplast (CP) data (left), mitochondrial (MT) data (middle) and nuclear (Nuc) data (right). Cladograms show topology only, branch lengths are not to scale. NC1, Neotropical clade 1; NC2, Neotropical clade 2.
Figure 2 in RESOLVING PHYLOGENETIC AND TAXONOMIC CONFLICT IN BEGONIA
Figure 2. Maximum likelihood phylogeny of Begonia based on a concatenated alignment of 1235 nuclear genes. Nodes have 100% fast bootstrap support, unless indicated. Section name abbreviations: AUG, Augustia; BAC, Baccabegonia; BEG, Begonia; BRA, Bracteibegonia; COE, Coelocentrum; DIP, Diploclinium; DON, Donaldia; ERM, Erminea; EXA, Exalabegonia; FLO, Flocciferae; GIR, Gireoudia; HAG, Haagea; LEP, Lepsia; LOA, Loasibegonia; NER, Nerviplacentaria; PET, Petermannia; PRI, Pritzelia; RID, Ridleyella; ROS, Rostrobegonia; SQA, Squamibegonia; TET, Tetraphila; WAG, Wagenaria.
Figure 1 in RESOLVING PHYLOGENETIC AND TAXONOMIC CONFLICT IN BEGONIA
Figure 1. Maximum likelihood phylogenies of Begonia based on chloroplast (CP) data (the ndhA intron, ndhF–rpl32 spacer and rpl32–trnL spacer; left) and mitochondrial (MT) data (the matR gene, nad1 intron and gene, nad7 introns and gene, and rps14–cob spacer; right). Asterisks represent fast bootstrap support of>90%. Tanglegram produced using the R package Phytools (Revell, 2012).
FIGURE 2 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 2. Syntopic species of Tropidurus found at the Reserva Particular do Patrimônio Natural Fazenda Pé da Serra, Serra do Arame, Ibotirama, Bahia, Brazil, and their respective habitats: (A, B) T. sertanejo, n. sp. (MZUSP 104274, allotype); (C, D) T. hispidus (MZUSP 104276); (E, F) T. pinima (MZUSP 104271).
FIGURE 6 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 6. Allotype of Tropidurus sertanejo, n. sp. (MZUSP 104274): (A) head in dorsal view; (B) head in ventral view; (C) head in lateral view; (D) dorsal body illustrating the spotted pattern typical of the new species; (E) ventral body showing the unpigmented underside of the thighs and cloacal flap characteristic of females.
FIGURE 5 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 5. Holotype of Tropidurus sertanejo, n. sp. (MZUSP 104273): (A) head in dorsal view; (B) head in ventral view showing intense pigmentation toward gular region; (C) head in lateral view; (D) dorsal body; (E) ventral body showing the typical dark flash marks on the underside of the thighs and cloacal flap of adult males.
FIGURE 15 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 15. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus on four mitochondrial (12S, 16S, CO1, Cyt b) and six nuclear loci (BACH1, kif24, NTF3, PRLR, PTPN, SNCAIP). Numbers associated to nodes refer to bootstrap values.
FIGURE 1. Taxonomic curve showing a in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 1. Taxonomic curve showing a steep, nonasymptotic increment in the number of species of the lizard genus Tropidurus described since 1820. Specimen of T. sertanejo, n. sp., MZUSP 104274 (allotype).
FIGURE 14 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 14. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus based on four nuclear (BACH1, kif24, NTF3, PRLR, PTPN, SNCAIP) loci. Numbers associated to nodes refer to bootstrap values.
FIGURE 13 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 13. Maximum parsimony (upper) and maximum likelihood trees (lower) of Tropidurus based on four mitochondrial (12S, 16S, CO1, Cyt b) loci. Numbers associated to nodes refer to bootstrap values.
FIGURE 11 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 11. Boxplot showing variation in scale counts among Tropidurus species (ordinated by mean): (Tcat) T. catalanensis, (Tchr) T. chromatops, (Tcoc) T. cocorobensis, (Tery) T. erythrocephalus, (Teth) T. etheridgei, (This) T. hispidus, (Thyg) T. hygomi, (Timb) T. imbituba, (Tins) T. insulanus, (Tita) T. itambere, (Tmon) T. montanus, (Tmuc) T. mucujensis, (Tore) T. oreadicus, (Tpsa) T. psammonastes, (Tser) T. sertanejo, n. sp. (highlighted in dark gray.), (Ttor) T. torquatus.
FIGURE 4 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 4. Measurements used for morphometric analyses of Tropidurus. Abbreviations: AL, arm length; EOS, ear opening–snout distance; FAL, forearm length; FOL, foot length; HDL, hand length; HH, head height; HW, head width; SL, shank length; SVL, snout-vent length; THL, thigh length; TL, tail length.
FIGURE 3 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 3. Map on left shows the distribution of the Brazilian biomes and highlights the State of Bahia, predominantly covered by the semiarid Caatinga. Map on right (altimetric profile) shows the distribution of Tropidurus sertanejo, n. sp.: northernmost dot indicates the type locality (RPPN Fazenda Pé da Serra, Serra do Arame, Ibotirama, Bahia: 12° 08′ 45.21 S, 43° 03′ 20.83 W) and southernmost dot indicates the only known additional locality of occurrence of the new species (Caetité, Bahia: 14° 04′ 17.82 S, 42° 29′ 48.33″ W).
FIGURE 12 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 12. Scatterplot of LD1 and LD2 generated by the discriminant analysis performed on the scale counts of Tropidurus. See table 8 for corresponding summary statistics. Tropidurus sertanejo, n. sp., highlighted in dark gray.
FIGURE 10 in A new Tropidurus (Tropiduridae) from the semiarid Brazilian Caatinga: evidence for conflicting signal between mitochondrial and nuclear loci affecting the phylogenetic reconstruction of South American collared lizards
FIGURE 10. Scatterplot of PC1 and PC2 generated by the principal component analyses and LD1 and LD2 generated by the size-free discriminant analyses performed on the log-transformed morphometric variables of Tropidurus. Tropidurus sertanejo, n. sp., highlighted in dark gray. See table 5 for corresponding summary statistics.
Interrogating genomic data in the phylogenetic placement of treeshrews reveals potential sources of conflict
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Data from: Phylogenetic conflict between species tree and maternally inherited gene trees in a clade of Emberiza buntings (Aves: Emberizidae)
<p>Different genomic regions may reflect conflicting phylogenetic topologies on account of incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four <em>Emberiza</em> species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of <em>Emberiza godlewskii</em> (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Phylogenetic analyses based on both the whole mitochondrial genome and ~39 kilobases from the non-recombining W chromosome reveal that the northern and southern populations of <em>E. godlewskii</em> are each sister to <em>E. cioides</em> and <em>E. cia</em>, respectively. In contrast, phylogenetic analysis based on genome-wide data support the monophyly of <em>E. godlewskii</em> with the following tree topology: (((<em>E. godlewskii</em>, <em>E. cia</em>), <em>E. cioides</em>), <em>E. jankowskii</em>).<em> </em>Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to <em>E. cioides</em> or introgression from an unsampled mitochondrial + W chromosomal lineage of <em>E. cioides</em> into northern <em>E. godlewskii </em>may explain the phylogenetic conflict between the species tree estimated from genome-wide data and mtDNA/W trees. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.</p>
Supplementary information for: The artefactual branch effect and phylogenetic conflict: Species delimitation with gene flow in mangrove pit vipers (Trimeresurus purpureomaculatus-erythrurus complex)
<p>Mangrove pit vipers of the <em>Trimeresurus</em> <em>purpureomaculatus</em>-<em>erythrurus</em> complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiated the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/ differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.</p>
Data from: Exploring conflicts in whole genome phylogenetics: A case study within Manakins (Aves: Pipridae)
<p>Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using an appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera <em>Antilophia</em> and <em>Chiroxiphia</em>. Previous studies suggest that <em>Antilophia</em> is nested within <em>Chiroxiphia</em>, though relationships among <em>Antilophia</em>+<em>Chiroxiphia</em> species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multi-species coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with two clades (<em>Antilophia</em>+<em>Chiroxiphia</em> and <em>Manacus</em>+<em>Pipra</em>+<em>Machaeopterus</em>) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting <em>Antilophia</em>+<em>Chiroxiphia</em>) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of <em>Antilophia</em>+<em>Chiroxiphia</em> or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of <em>Antilophia</em>+<em>Chiroxiphia</em>. We also found evidence for introgression that may have contributed to the discordant topologies we observe in <em>Antilophia</em>+<em>Chiroxiphia</em> and led to deviations from expectations given the multi-species coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting and reticulation events.</p>
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