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@ -84,7 +87,7 @@ group polytomy
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Our approach identified the optimal number of gene tree clusters in our data as three. Cluster 1 contained 72 loci (33 protein-coding, 39 non-coding) with a mean length of 955 bp, and a mean number of parsimony-informative sites of 141. Cluster 2 contained 50 loci (21 protein-coding, 29 non-coding) with a mean length of 276 bp, and a mean number of parsimony-informative sites of 44. Cluster 3 contained 26 loci (17 protein-coding, 9 non-coding) with a mean length of 378 bp, and a mean number of parsimony-informative sites of 66. Re-estimating the phylogeny for each of the three clusters produced trees with no supported incongruence between, for both IQ-TREE (Supplementary
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) and ASTRAL phylogenies (see files under Data availability). RAxML gene trees from Clusters 1 and 2 were significantly longer than those in Cluster 3 (Dunn’s test; Bonferroni adjusted
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@ -98,7 +101,7 @@ and
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= 5.52 × 10
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respectively; Supplementary
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). Bootstrap support was significantly different among all clusters, with support values in Cluster 1 being markedly higher than those in Clusters 2 and 3 (Dunn’s test; Bonferroni adjusted
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@ -130,7 +133,7 @@ for
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2–
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3;
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).
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<paragraph id="6B5336FCE223FF93678FFAD4EBA8F8AC" blockId="16.[98,770,1361,1932]" pageId="16" pageNumber="371">Across all loci, the mean percentage of fully resolved quartets (i.e. quartets falling into Regions 1, 2 and 3 of the likelihood-mapping plot) was 53%. The means for partly resolved quartets (Regions 4, 5 and 6) and unresolved quartets (Region 7) were 4 and 43% respectively. The subset of loci with>50% fully resolved quartets contained 102 loci with a mean length of 851 bp, and a mean number of parsimony-informative sites of 140. The subset of loci with>60% fully resolved quartets contained 63 loci with a mean length of 1056 bp, and a mean number of parsimony-informative sites of 178. The subset of loci with>70% fully resolved quartets contained 22 loci with a mean length of 1490 bp, and a mean number of parsimony-informative sites of 302.</paragraph>
|
||||
<paragraph id="6B5336FCE223FF93678FF894EE77FB4C" blockId="16.[98,770,1361,1932]" lastBlockId="16.[818,1490,532,1228]" pageId="16" pageNumber="371">
|
||||
Phylogenetic analysis of each of the subsets resulted in trees with identical topologies that were congruent with the phylogeny produced in the analysis of the unpartitioned full dataset (i.e.
|
||||
<figureCitation id="F3D72A79E223FF9364B2FDB4E8BBFDAC" box="[959,1023,532,556]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" pageId="16" pageNumber="371">Fig. 3</figureCitation>
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||||
<figureCitation id="F3D72A79E223FF9364B2FDB4E8BBFDAC" box="[959,1023,532,556]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" figureDoi="http://doi.org/10.5281/zenodo.13835473" httpUri="https://zenodo.org/record/13835473/files/figure.png" pageId="16" pageNumber="371">Fig. 3</figureCitation>
|
||||
). In general, all subset trees had slightly lower branch support than the full-dataset tree. Among subset trees, the>70% tree had the lowest branch support, with exception to the placement of
|
||||
<taxonomicName id="ACEC4D7FE223FF9363D9FDD4EE96FD0C" box="[1236,1490,628,652]" class="Magnoliopsida" family="Rutaceae" genus="Philotheca" kingdom="Plantae" order="Sapindales" pageId="16" pageNumber="371" phylum="Tracheophyta" rank="species" species="angustifolia">
|
||||
<emphasis id="5998EAEEE223FF9363D9FDD4EE96FD0C" bold="true" box="[1236,1490,628,652]" italics="true" pageId="16" pageNumber="371">Philotheca angustifolia</emphasis>
|
||||
|
|
@ -155,7 +158,7 @@ and
|
|||
<emphasis id="5998EAEEE223FF936355FD34EF93FD2C" bold="true" box="[1112,1239,660,684]" italics="true" pageId="16" pageNumber="371">P. difformis</emphasis>
|
||||
</taxonomicName>
|
||||
with low-to-moderate support (UFBoot: 91; SH-aLRT: 82.9). The>50 and>60% trees did not resolve the position of this species. Despite the removal of potentially noisy or discordant loci, none of the subset trees contained a supported resolution for the backbone polytomy; the>60% subset tree displayed the highest support for short branches of the polytomy, but these branches were still unsupported and resulted in star-like resolution of the polytomy in our network analysis (
|
||||
<figureCitation id="F3D72A79E223FF936436FC14E8CDFC4C" box="[827,905,948,972]" captionStart="Fig" captionStartId="18.[203,240,1180,1203]" captionTargetBox="[130,1485,510,1165]" captionTargetId="graphics-1812@18.[586,1617,337,1258]" captionTargetPageId="18" captionText="Fig. 5. Results of the likelihood-mapping analysis of loci. (a) Plot of phylogenetic informativeness of individual loci, where a higher percentage of fully resolved quartets for a locus indicates greater support for tree-like evolution. Dashed lines on the plot indicate the three cut-off values that were tested for potentially improving phylogenetic resolution of the polytomy (i.e. 50, 60 and 70%). Bars along the x-axis denote the cluster that each locus was placed in during the analysis of tree space; some loci were excluded from the tree-space analysis, owing to incomplete representation of samples. (b) Phylogenetic network (NeighborNet) showing splits of the backbone polytomy; constructed from a concatenated alignment of all loci with>60% of quartets fully resolved. For Crowea, EA, eastern Australia; WA, western Australia." pageId="16" pageNumber="371">
|
||||
<figureCitation id="F3D72A79E223FF936436FC14E8CDFC4C" box="[827,905,948,972]" captionStart="Fig" captionStartId="18.[203,240,1180,1203]" captionTargetBox="[130,1485,510,1165]" captionTargetId="graphics-1812@18.[586,1617,337,1258]" captionTargetPageId="18" captionText="Fig. 5. Results of the likelihood-mapping analysis of loci. (a) Plot of phylogenetic informativeness of individual loci, where a higher percentage of fully resolved quartets for a locus indicates greater support for tree-like evolution. Dashed lines on the plot indicate the three cut-off values that were tested for potentially improving phylogenetic resolution of the polytomy (i.e. 50, 60 and 70%). Bars along the x-axis denote the cluster that each locus was placed in during the analysis of tree space; some loci were excluded from the tree-space analysis, owing to incomplete representation of samples. (b) Phylogenetic network (NeighborNet) showing splits of the backbone polytomy; constructed from a concatenated alignment of all loci with>60% of quartets fully resolved. For Crowea, EA, eastern Australia; WA, western Australia." figureDoi="http://doi.org/10.5281/zenodo.13835486" httpUri="https://zenodo.org/record/13835486/files/figure.png" pageId="16" pageNumber="371">
|
||||
Fig. 5
|
||||
<emphasis id="5998EAEEE223FF936470FC14E8CDFC4C" bold="true" box="[893,905,948,972]" italics="true" pageId="16" pageNumber="371">b</emphasis>
|
||||
</figureCitation>
|
||||
|
|
@ -198,17 +201,17 @@ rank sum test;
|
|||
</paragraph>
|
||||
<paragraph id="6B5336FCE223FF91645FFAB4EA3EF9EC" blockId="16.[818,1490,1265,1932]" lastBlockId="18.[98,770,1428,1644]" lastPageId="18" lastPageNumber="373" pageId="16" pageNumber="371">
|
||||
Owing to high UFBoot and posterior probability support for four clades forming the backbone polytomy, our tree-topology testing investigated support for the 15 possible relationships among these clades (
|
||||
<figureCitation id="F3D72A79E223FF9363C9FAD4EE50FA0B" box="[1220,1300,1396,1420]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." pageId="16" pageNumber="371">
|
||||
<figureCitation id="F3D72A79E223FF9363C9FAD4EE50FA0B" box="[1220,1300,1396,1420]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." figureDoi="http://doi.org/10.5281/zenodo.13835488" httpUri="https://zenodo.org/record/13835488/files/figure.png" pageId="16" pageNumber="371">
|
||||
Fig. 6
|
||||
<emphasis id="5998EAEEE223FF93620AFAD4EE50FA0B" bold="true" box="[1287,1300,1396,1419]" italics="true" pageId="16" pageNumber="371">a</emphasis>
|
||||
</figureCitation>
|
||||
). Log-likelihood values for each topology ranged from −494 970.83 to −494 975.48. Expectedly, the topology of the most likely tree used as input was found to have the highest log-likelihood (−494 970.83); this topology was identical to the 15th possible resolution of the polytomy (
|
||||
<figureCitation id="F3D72A79E223FF93627DF9B4EE84F9AB" box="[1392,1472,1556,1580]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." pageId="16" pageNumber="371">
|
||||
<figureCitation id="F3D72A79E223FF93627DF9B4EE84F9AB" box="[1392,1472,1556,1580]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." figureDoi="http://doi.org/10.5281/zenodo.13835488" httpUri="https://zenodo.org/record/13835488/files/figure.png" pageId="16" pageNumber="371">
|
||||
Fig. 6
|
||||
<emphasis id="5998EAEEE223FF9362BEF9B4EE84F9AB" bold="true" box="[1459,1472,1556,1579]" italics="true" pageId="16" pageNumber="371">a</emphasis>
|
||||
</figureCitation>
|
||||
). Five topologies were found to have slightly higher log-likelihoods than the others (
|
||||
<figureCitation id="F3D72A79E223FF936376F9F4EF8DF9EC" box="[1147,1225,1620,1644]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." pageId="16" pageNumber="371">
|
||||
<figureCitation id="F3D72A79E223FF936376F9F4EF8DF9EC" box="[1147,1225,1620,1644]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." figureDoi="http://doi.org/10.5281/zenodo.13835488" httpUri="https://zenodo.org/record/13835488/files/figure.png" pageId="16" pageNumber="371">
|
||||
Fig. 6
|
||||
<emphasis id="5998EAEEE223FF9363B0F9F4EF8DF9EC" bold="true" box="[1213,1225,1620,1644]" italics="true" pageId="16" pageNumber="371">b</emphasis>
|
||||
</figureCitation>
|
||||
|
|
@ -242,14 +245,14 @@ tests (
|
|||
.
|
||||
</paragraph>
|
||||
</subSubSection>
|
||||
<caption id="3F936674E222FF926794F8B4EA8FF8AB" box="[153,459,1811,1835]" pageId="17" pageNumber="372" startId="17.[153,190,1812,1835]" targetBox="[153,1434,185,1781]" targetPageId="17" targetType="figure">
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||||
<caption id="3F936674E222FF926794F8B4EA8FF8AB" ID-DOI="http://doi.org/10.5281/zenodo.13835479" ID-Zenodo-Dep="13835479" box="[153,459,1811,1835]" httpUri="https://zenodo.org/record/13835479/files/figure.png" pageId="17" pageNumber="372" startId="17.[153,190,1812,1835]" targetBox="[153,1434,185,1781]" targetPageId="17" targetType="figure">
|
||||
<paragraph id="6B5336FCE222FF926794F8B4EA8FF8AB" blockId="17.[153,459,1811,1835]" box="[153,459,1811,1835]" pageId="17" pageNumber="372">
|
||||
Fig. 4. (
|
||||
<emphasis id="5998EAEEE222FF9267F0F8B3EA80F8AB" bold="true" box="[253,452,1811,1835]" italics="true" pageId="17" pageNumber="372">Caption on next page</emphasis>
|
||||
)
|
||||
</paragraph>
|
||||
</caption>
|
||||
<caption id="3F936674E221FF91676FFF15E9AEFE1A" pageId="18" pageNumber="373" startId="18.[98,135,181,204]" targetBox="[153,1434,185,1781]" targetPageId="17" targetType="figure">
|
||||
<caption id="3F936674E221FF91676FFF15E9AEFE1A" ID-DOI="http://doi.org/10.5281/zenodo.13835483" ID-Zenodo-Dep="13835483" httpUri="https://zenodo.org/record/13835483/files/figure.png" pageId="18" pageNumber="373" startId="18.[98,135,181,204]" targetBox="[153,1434,185,1781]" targetPageId="17" targetType="figure">
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||||
<paragraph id="6B5336FCE221FF91676FFF15E9AEFE1A" blockId="18.[98,1491,181,410]" pageId="18" pageNumber="373">
|
||||
Fig. 4. Phylogenetic relationships in Clade 1. Maximum-likelihood phylogeny produced from IQ-TREE analysis of the ‘supermatrix’ alignment of combined full plastome and Sanger sequences. UFboot support for branches is positioned above posterior probabilities from the MrBayes 50% majority-rule consensus tree of the same dataset. Relationships in other clades are identical to those in Fig. 3. Unsupported short branches in the backbone of the
|
||||
<taxonomicName id="ACEC4D7FE221FF916641FEADEAF5FEA4" box="[332,433,269,292]" class="Magnoliopsida" family="Rutaceae" genus="Eriostemon" kingdom="Plantae" order="Sapindales" pageId="18" pageNumber="373" phylum="Tracheophyta" rank="genus">
|
||||
|
|
@ -284,7 +287,7 @@ section
|
|||
), as discussed in the text.
|
||||
</paragraph>
|
||||
</caption>
|
||||
<caption id="3F936674E221FF9167C6FB3CEE03FAE3" pageId="18" pageNumber="373" startId="18.[203,240,1180,1203]" targetBox="[130,1485,510,1165]" targetPageId="18" targetType="figure">
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||||
<caption id="3F936674E221FF9167C6FB3CEE03FAE3" ID-DOI="http://doi.org/10.5281/zenodo.13835486" ID-Zenodo-Dep="13835486" httpUri="https://zenodo.org/record/13835486/files/figure.png" pageId="18" pageNumber="373" startId="18.[203,240,1180,1203]" targetBox="[130,1485,510,1165]" targetPageId="18" targetType="figure">
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||||
<paragraph id="6B5336FCE221FF9167C6FB3CEE03FAE3" blockId="18.[203,1385,1180,1379]" pageId="18" pageNumber="373">
|
||||
Fig. 5. Results of the likelihood-mapping analysis of loci. (
|
||||
<emphasis id="5998EAEEE221FF916405FB3CE857FB33" bold="true" box="[776,787,1180,1203]" italics="true" pageId="18" pageNumber="373">a</emphasis>
|
||||
|
|
@ -433,7 +436,7 @@ Duretto
|
|||
2023
|
||||
</bibRefCitation>
|
||||
; indicated on
|
||||
<figureCitation id="F3D72A79E220FF9066F1FA74E906FA6C" box="[508,578,1492,1516]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" pageId="19" pageNumber="374">Fig. 3</figureCitation>
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||||
<figureCitation id="F3D72A79E220FF9066F1FA74E906FA6C" box="[508,578,1492,1516]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" figureDoi="http://doi.org/10.5281/zenodo.13835473" httpUri="https://zenodo.org/record/13835473/files/figure.png" pageId="19" pageNumber="374">Fig. 3</figureCitation>
|
||||
). The following sections discuss some relationships, supported here, that are noteworthy; relationships in the
|
||||
<taxonomicName id="ACEC4D7FE220FF906534F9B3E9E8F9AB" box="[569,684,1555,1579]" class="Magnoliopsida" family="Rutaceae" genus="Phebalium" kingdom="Plantae" order="Sapindales" pageId="19" pageNumber="374" phylum="Tracheophyta" rank="genus">
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||||
<emphasis id="5998EAEEE220FF906534F9B3E9E8F9AB" bold="true" box="[569,684,1555,1579]" italics="true" pageId="19" pageNumber="374">Phebalium</emphasis>
|
||||
|
|
|
|||
|
|
@ -1,68 +1,71 @@
|
|||
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@ -156,7 +159,7 @@ and
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<emphasis id="5998EAEEE226FF9667C2FAB4EAEBFAAC" bold="true" box="[207,431,1300,1324]" italics="true" pageId="21" pageNumber="376">Muiriantha hassellii</emphasis>
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</taxonomicName>
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has pendulous flowers with imbricate yellowish-green petals that form an elongated tube (
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<figureCitation id="F3D72A79E226FF9667A4FAF4EBBFFAEB" box="[169,251,1364,1388]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." pageId="21" pageNumber="376">
|
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<figureCitation id="F3D72A79E226FF9667A4FAF4EBBFFAEB" box="[169,251,1364,1388]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." figureDoi="http://doi.org/10.5281/zenodo.13835494" httpUri="https://zenodo.org/record/13835494/files/figure.png" pageId="21" pageNumber="376">
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Fig. 7
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<emphasis id="5998EAEEE226FF9667E3FAF4EBBFFAEB" bold="true" box="[238,251,1364,1387]" italics="true" pageId="21" pageNumber="376">a</emphasis>
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</figureCitation>
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|
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@ -167,7 +170,7 @@ section
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<emphasis id="5998EAEEE226FF96676FFAD4EA45FA0C" bold="true" box="[98,257,1396,1420]" italics="true" pageId="21" pageNumber="376">Cyanochlamys</emphasis>
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</taxonomicName>
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are borne erectly, with petals spreading and ranging from pink to blue in colour (
|
||||
<figureCitation id="F3D72A79E226FF96650AFA34E92BFA2B" box="[519,623,1428,1452]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." pageId="21" pageNumber="376">
|
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<figureCitation id="F3D72A79E226FF96650AFA34E92BFA2B" box="[519,623,1428,1452]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." figureDoi="http://doi.org/10.5281/zenodo.13835494" httpUri="https://zenodo.org/record/13835494/files/figure.png" pageId="21" pageNumber="376">
|
||||
Fig. 7
|
||||
<emphasis id="5998EAEEE226FF966545FA34E910FA2C" bold="true" box="[584,596,1428,1452]" italics="true" pageId="21" pageNumber="376">b</emphasis>
|
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,
|
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|
|
@ -242,7 +245,7 @@ and
|
|||
<emphasis id="5998EAEEE226FF96651BF8F4E9D5F8EC" bold="true" box="[534,657,1876,1900]" italics="true" pageId="21" pageNumber="376">Muiriantha</emphasis>
|
||||
</taxonomicName>
|
||||
, they are broadly similar in having a subshrub habit and leaves with a somewhat papery texture. Further morphological examination by the authors has also shown similarities in carpel surfaces and branchlet indumenta (
|
||||
<figureCitation id="F3D72A79E226FF9663CEFF54EE47FE8B" box="[1219,1283,244,268]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." pageId="21" pageNumber="376">Fig. 7</figureCitation>
|
||||
<figureCitation id="F3D72A79E226FF9663CEFF54EE47FE8B" box="[1219,1283,244,268]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." figureDoi="http://doi.org/10.5281/zenodo.13835494" httpUri="https://zenodo.org/record/13835494/files/figure.png" pageId="21" pageNumber="376">Fig. 7</figureCitation>
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).
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</paragraph>
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<paragraph id="6B5336FCE226FF96645FFEB5EF9BFE6D" blockId="21.[818,1490,180,1452]" pageId="21" pageNumber="376">
|
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|
|
@ -262,7 +265,7 @@ section
|
|||
, the abaxial surface of the carpels is conspicuously pitted with small glands (
|
||||
<bibRefCitation id="0F7D4B0DE226FF96649DFEF4EF51FEEC" author="Bayly MJ" box="[912,1045,340,364]" pageId="21" pageNumber="376" refId="ref19349" refString="Bayly MJ (2001) A cladistic and biogeographic analysis of Philotheca (Rutaceae) and allied genera. PhD thesis, The University of Melbourne, Melbourne, Vic., Australia. Available at http: // hdl. handle. net / 11343 / 37369" type="url" year="2001">Bayly 2001</bibRefCitation>
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;
|
||||
<figureCitation id="F3D72A79E226FF966324FEF4EFD4FEEC" box="[1065,1168,340,364]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." pageId="21" pageNumber="376">
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<figureCitation id="F3D72A79E226FF966324FEF4EFD4FEEC" box="[1065,1168,340,364]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." figureDoi="http://doi.org/10.5281/zenodo.13835494" httpUri="https://zenodo.org/record/13835494/files/figure.png" pageId="21" pageNumber="376">
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Fig. 7
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<emphasis id="5998EAEEE226FF966360FEF4EFD4FEEC" bold="true" box="[1133,1168,340,364]" italics="true" pageId="21" pageNumber="376">d–f</emphasis>
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</figureCitation>
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|
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@ -354,7 +357,7 @@ section
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|||
. Fasciculate hairs of this
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(
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<figureCitation id="F3D72A79E226FF966391FC14EE44FC4C" box="[1180,1280,948,972]" captionStart="Fig" captionStartId="22.[170,207,1649,1672]" captionTargetBox="[170,1418,185,1619]" captionTargetId="figure-66@22.[170,1418,185,1620]" captionTargetPageId="22" captionText="Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of Muiriantha and Philotheca section Cyanochlamys (voucher numbers indicated in brackets): (a, d, f) Muiriantha hassellii [MJB 2574, MELUD155083a], (b, e, h) Philotheca nodiflora subsp. lasiocalyx [b, e, MJB 108, MELU; h, MJB 1962, MELUD105840a], (c, f, i) Philotheca spicata [c, f, MJB 9, MELU; i, MJB 10, MELU]. Scale bars: 500 μm, in micrographs of carpels (inset close-up images of pits are not to scale), and 100 μm, in micrographs of hairs (arrows indicate fasciculate hairs in h, i that are obscured by other hairs)." pageId="21" pageNumber="376">
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<emphasis id="5998EAEEE226FF96643FF8F4E8E8F8EC" bold="true" box="[818,940,1876,1900]" italics="true" pageId="21" pageNumber="376">Eriostemon</emphasis>
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group and readily recognisable in being ellipsoid and laterally flattened with a linear hilum on the adaxial face and having a basal raphe and chalazal region (
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<figureCitation id="F3D72A79E225FF9565B4F894E9BEF8CC" box="[697,762,1844,1868]" captionStart="Fig" captionStartId="23.[1097,1134,912,935]" captionTargetBox="[98,1077,155,1517]" captionTargetId="figure-203@23.[98,976,225,1516]" captionTargetPageId="23" captionText="Fig. 8. Seed morphology in Clade 1, showing the adaxially central raphe in Philotheca section Philotheca, Drummondita and Geleznowia, and the basal raphe in Philotheca section Erionema. (a–c) Seeds typical of P. section Philotheca [P. linearis; G.J. White s.n., NE 52727]. (d–f) Seeds typical of Drummondita [D. longifolia; H. Demarz 10361, PERTH 959707]. (g–i) Seeds typical of Geleznowia [G. verru- cosa; L. Broadhurst 14, PERTH 5547822]. (j–l) Seeds typical of P. section Erionema [P. verrucosa; MJB 249, HO523410]. (a, d, g, j) Lateral views. (b, e, h, k) Adaxial views. (c, f, i, l) Longitudinal sec- tions through the raphe. (a, g) Drawn with the placental portion of endocarp still attached to the seed; for all other draw- ings the placental endocarp was removed. Drawings are modified from Bayly (2001) and are not to scale." pageId="22" pageNumber="377">Fig. 8</figureCitation>
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<figureCitation id="F3D72A79E225FF9565B4F894E9BEF8CC" box="[697,762,1844,1868]" captionStart="Fig" captionStartId="23.[1097,1134,912,935]" captionTargetBox="[98,1077,155,1517]" captionTargetId="figure-203@23.[98,976,225,1516]" captionTargetPageId="23" captionText="Fig. 8. Seed morphology in Clade 1, showing the adaxially central raphe in Philotheca section Philotheca, Drummondita and Geleznowia, and the basal raphe in Philotheca section Erionema. (a–c) Seeds typical of P. section Philotheca [P. linearis; G.J. White s.n., NE 52727]. (d–f) Seeds typical of Drummondita [D. longifolia; H. Demarz 10361, PERTH 959707]. (g–i) Seeds typical of Geleznowia [G. verru- cosa; L. Broadhurst 14, PERTH 5547822]. (j–l) Seeds typical of P. section Erionema [P. verrucosa; MJB 249, HO523410]. (a, d, g, j) Lateral views. (b, e, h, k) Adaxial views. (c, f, i, l) Longitudinal sec- tions through the raphe. (a, g) Drawn with the placental portion of endocarp still attached to the seed; for all other draw- ings the placental endocarp was removed. Drawings are modified from Bayly (2001) and are not to scale." figureDoi="http://doi.org/10.5281/zenodo.13835498" httpUri="https://zenodo.org/record/13835498/files/figure.png" pageId="22" pageNumber="377">Fig. 8</figureCitation>
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;
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<bibRefCitation id="0F7D4B0DE225FF95676FF8F4EBB9F8EB" author="Wilson PG" box="[98,253,1876,1900]" pageId="22" pageNumber="377" pagination="239 - 265" refId="ref23116" refString="Wilson PG (1998 a) A taxonomic review of the genera Eriostemon and Philotheca (Rutaceae: Boronieae). Nuytsia 12, 239 - 265." type="journal article" year="1998">
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Wilson 1998
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@ -181,14 +184,14 @@ and
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<emphasis id="5998EAEEE225FF956517F8D3E9DCF80B" bold="true" box="[538,664,1907,1931]" italics="true" pageId="22" pageNumber="377">Geleznowia</emphasis>
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(
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<figureCitation id="F3D72A79E225FF9565A0F8D4E9B5F80C" box="[685,753,1908,1932]" captionStart="Fig" captionStartId="23.[1097,1134,912,935]" captionTargetBox="[98,1077,155,1517]" captionTargetId="figure-203@23.[98,976,225,1516]" captionTargetPageId="23" captionText="Fig. 8. Seed morphology in Clade 1, showing the adaxially central raphe in Philotheca section Philotheca, Drummondita and Geleznowia, and the basal raphe in Philotheca section Erionema. (a–c) Seeds typical of P. section Philotheca [P. linearis; G.J. White s.n., NE 52727]. (d–f) Seeds typical of Drummondita [D. longifolia; H. Demarz 10361, PERTH 959707]. (g–i) Seeds typical of Geleznowia [G. verru- cosa; L. Broadhurst 14, PERTH 5547822]. (j–l) Seeds typical of P. section Erionema [P. verrucosa; MJB 249, HO523410]. (a, d, g, j) Lateral views. (b, e, h, k) Adaxial views. (c, f, i, l) Longitudinal sec- tions through the raphe. (a, g) Drawn with the placental portion of endocarp still attached to the seed; for all other draw- ings the placental endocarp was removed. Drawings are modified from Bayly (2001) and are not to scale." pageId="22" pageNumber="377">Fig. 8</figureCitation>
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<figureCitation id="F3D72A79E225FF9565A0F8D4E9B5F80C" box="[685,753,1908,1932]" captionStart="Fig" captionStartId="23.[1097,1134,912,935]" captionTargetBox="[98,1077,155,1517]" captionTargetId="figure-203@23.[98,976,225,1516]" captionTargetPageId="23" captionText="Fig. 8. Seed morphology in Clade 1, showing the adaxially central raphe in Philotheca section Philotheca, Drummondita and Geleznowia, and the basal raphe in Philotheca section Erionema. (a–c) Seeds typical of P. section Philotheca [P. linearis; G.J. White s.n., NE 52727]. (d–f) Seeds typical of Drummondita [D. longifolia; H. Demarz 10361, PERTH 959707]. (g–i) Seeds typical of Geleznowia [G. verru- cosa; L. Broadhurst 14, PERTH 5547822]. (j–l) Seeds typical of P. section Erionema [P. verrucosa; MJB 249, HO523410]. (a, d, g, j) Lateral views. (b, e, h, k) Adaxial views. (c, f, i, l) Longitudinal sec- tions through the raphe. (a, g) Drawn with the placental portion of endocarp still attached to the seed; for all other draw- ings the placental endocarp was removed. Drawings are modified from Bayly (2001) and are not to scale." figureDoi="http://doi.org/10.5281/zenodo.13835498" httpUri="https://zenodo.org/record/13835498/files/figure.png" pageId="22" pageNumber="377">Fig. 8</figureCitation>
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||||
), which share a strong morphological resemblance in comparison to other members of the
|
||||
<taxonomicName id="ACEC4D7FE225FF956370F8F4EFB3F8EC" box="[1149,1271,1876,1900]" class="Magnoliopsida" family="Rutaceae" genus="Eriostemon" kingdom="Plantae" order="Sapindales" pageId="22" pageNumber="377" phylum="Tracheophyta" rank="genus">
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||||
<emphasis id="5998EAEEE225FF956370F8F4EFB3F8EC" bold="true" box="[1149,1271,1876,1900]" italics="true" pageId="22" pageNumber="377">Eriostemon</emphasis>
|
||||
</taxonomicName>
|
||||
group, are more or less reniform, substantially thicker than their length, have a smaller hilum that is round to deltoid and located, together with the raphe, on the adaxial face of the seed.
|
||||
</paragraph>
|
||||
<caption id="3F936674E225FF9567A7F9D1E897F97E" pageId="22" pageNumber="377" startId="22.[170,207,1649,1672]" targetBox="[170,1418,185,1619]" targetPageId="22" targetType="figure">
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<paragraph id="6B5336FCE225FF9567A7F9D1E897F97E" blockId="22.[170,1418,1649,1790]" pageId="22" pageNumber="377">
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||||
Fig. 7. Flowers, carpels (with pitted surfaces), and fasciculate stem hairs of
|
||||
<taxonomicName id="ACEC4D7FE225FF9564B0F9D1EF64F908" box="[957,1056,1649,1672]" class="Magnoliopsida" family="Rutaceae" genus="Muiriantha" kingdom="Plantae" order="Sapindales" pageId="22" pageNumber="377" phylum="Tracheophyta" rank="genus">
|
||||
|
|
@ -261,7 +264,7 @@ subsp.
|
|||
that are obscured by other hairs).
|
||||
</paragraph>
|
||||
</caption>
|
||||
<caption id="3F936674E224FF946344FC30EE4AFA72" pageId="23" pageNumber="378" startId="23.[1097,1134,912,935]" targetBox="[98,1077,155,1517]" targetPageId="23" targetType="figure">
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<caption id="3F936674E224FF946344FC30EE4AFA72" ID-DOI="http://doi.org/10.5281/zenodo.13835498" ID-Zenodo-Dep="13835498" httpUri="https://zenodo.org/record/13835498/files/figure.png" pageId="23" pageNumber="378" startId="23.[1097,1134,912,935]" targetBox="[98,1077,155,1517]" targetPageId="23" targetType="figure">
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<paragraph id="6B5336FCE224FF946344FC30EE4AFA72" blockId="23.[1097,1490,912,1522]" pageId="23" pageNumber="378">
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Fig. 8. Seed morphology in Clade 1, showing the adaxially central raphe in
|
||||
<taxonomicName id="ACEC4D7FE224FF946344FC6BEE0EFC62" authority="section Philotheca" box="[1097,1354,971,994]" class="Magnoliopsida" family="Rutaceae" genus="Philotheca" kingdom="Plantae" order="Sapindales" pageId="23" pageNumber="378" phylum="Tracheophyta" rank="section" section="Philotheca">
|
||||
|
|
@ -388,7 +391,7 @@ and one sister to
|
|||
<emphasis id="5998EAEEE224FF9466CAF8B3E901F8AB" bold="true" box="[455,581,1811,1835]" italics="true" pageId="23" pageNumber="378">Geleznowia</emphasis>
|
||||
</taxonomicName>
|
||||
(
|
||||
<figureCitation id="F3D72A79E224FF94655AF8B4E9D3F8AC" box="[599,663,1812,1836]" captionStart="Fig" captionStartId="17.[153,190,1812,1835]" captionTargetBox="[153,1434,185,1781]" captionTargetId="graphics-2@17.[153,1397,185,1755]" captionTargetPageId="17" captionText="Fig. 4. (Caption on next page)" pageId="23" pageNumber="378">Fig. 4</figureCitation>
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<figureCitation id="F3D72A79E224FF94655AF8B4E9D3F8AC" box="[599,663,1812,1836]" captionStart="Fig" captionStartId="17.[153,190,1812,1835]" captionTargetBox="[153,1434,185,1781]" captionTargetId="graphics-2@17.[153,1397,185,1755]" captionTargetPageId="17" captionText="Fig. 4. (Caption on next page)" figureDoi="http://doi.org/10.5281/zenodo.13835479" httpUri="https://zenodo.org/record/13835479/files/figure.png" pageId="23" pageNumber="378">Fig. 4</figureCitation>
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||||
).
|
||||
</paragraph>
|
||||
<paragraph id="6B5336FCE224FF9B678FF894EBBEFE0C" blockId="23.[98,770,1588,1932]" lastBlockId="24.[98,770,180,1452]" lastPageId="24" lastPageNumber="379" pageId="23" pageNumber="378">
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|
|
@ -424,7 +427,7 @@ Wilson (1998
|
|||
</taxonomicName>
|
||||
<taxonomicNameLabel id="42AB5795E224FF946294F9F4EE89F9EB" box="[1433,1485,1620,1643]" pageId="23" pageNumber="378" sensu="stricto">s.str.</taxonomicNameLabel>
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;
|
||||
<figureCitation id="F3D72A79E224FF94643FF9D4E82BF90C" box="[818,879,1652,1676]" captionStart="Fig" captionStartId="17.[153,190,1812,1835]" captionTargetBox="[153,1434,185,1781]" captionTargetId="graphics-2@17.[153,1397,185,1755]" captionTargetPageId="17" captionText="Fig. 4. (Caption on next page)" pageId="23" pageNumber="378">Fig. 4</figureCitation>
|
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<figureCitation id="F3D72A79E224FF94643FF9D4E82BF90C" box="[818,879,1652,1676]" captionStart="Fig" captionStartId="17.[153,190,1812,1835]" captionTargetBox="[153,1434,185,1781]" captionTargetId="graphics-2@17.[153,1397,185,1755]" captionTargetPageId="17" captionText="Fig. 4. (Caption on next page)" figureDoi="http://doi.org/10.5281/zenodo.13835479" httpUri="https://zenodo.org/record/13835479/files/figure.png" pageId="23" pageNumber="378">Fig. 4</figureCitation>
|
||||
, black triangle), first circumscribed by
|
||||
<bibRefCitation id="0F7D4B0DE224FF946217F9D4EE8EF90C" author="Bentham G" box="[1306,1482,1652,1676]" pageId="23" pageNumber="378" refId="ref19503" refString="Bentham G (1863) ' Flora australiensis. Vol. 1. ' (Lovell Reeve: London, UK)" type="book" year="1863">Bentham (1863)</bibRefCitation>
|
||||
, included only species with 10 fertile, monadelphous stamens and a spreading corolla.
|
||||
|
|
@ -559,7 +562,7 @@ are fused only very minutely at the base (
|
|||
by
|
||||
<bibRefCitation id="0F7D4B0DE22BFF9B656EFD34E9BEFD2C" author="Bayly MJ" box="[611,762,660,684]" pageId="24" pageNumber="379" refId="ref19349" refString="Bayly MJ (2001) A cladistic and biogeographic analysis of Philotheca (Rutaceae) and allied genera. PhD thesis, The University of Melbourne, Melbourne, Vic., Australia. Available at http: // hdl. handle. net / 11343 / 37369" type="url" year="2001">Bayly (2001)</bibRefCitation>
|
||||
; the free nature of filaments in this species was verified in the current study by using scanning electron microscopy (see Supplementary
|
||||
<figureCitation id="F3D72A79E22BFF9B6645FD54EADDFC8C" box="[328,409,756,780]" captionStart="Fig" captionStartId="18.[203,240,1180,1203]" captionTargetBox="[130,1485,510,1165]" captionTargetId="graphics-1812@18.[586,1617,337,1258]" captionTargetPageId="18" captionText="Fig. 5. Results of the likelihood-mapping analysis of loci. (a) Plot of phylogenetic informativeness of individual loci, where a higher percentage of fully resolved quartets for a locus indicates greater support for tree-like evolution. Dashed lines on the plot indicate the three cut-off values that were tested for potentially improving phylogenetic resolution of the polytomy (i.e. 50, 60 and 70%). Bars along the x-axis denote the cluster that each locus was placed in during the analysis of tree space; some loci were excluded from the tree-space analysis, owing to incomplete representation of samples. (b) Phylogenetic network (NeighborNet) showing splits of the backbone polytomy; constructed from a concatenated alignment of all loci with>60% of quartets fully resolved. For Crowea, EA, eastern Australia; WA, western Australia." pageId="24" pageNumber="379">Fig. S5</figureCitation>
|
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<figureCitation id="F3D72A79E22BFF9B6645FD54EADDFC8C" box="[328,409,756,780]" captionStart="Fig" captionStartId="18.[203,240,1180,1203]" captionTargetBox="[130,1485,510,1165]" captionTargetId="graphics-1812@18.[586,1617,337,1258]" captionTargetPageId="18" captionText="Fig. 5. Results of the likelihood-mapping analysis of loci. (a) Plot of phylogenetic informativeness of individual loci, where a higher percentage of fully resolved quartets for a locus indicates greater support for tree-like evolution. Dashed lines on the plot indicate the three cut-off values that were tested for potentially improving phylogenetic resolution of the polytomy (i.e. 50, 60 and 70%). Bars along the x-axis denote the cluster that each locus was placed in during the analysis of tree space; some loci were excluded from the tree-space analysis, owing to incomplete representation of samples. (b) Phylogenetic network (NeighborNet) showing splits of the backbone polytomy; constructed from a concatenated alignment of all loci with>60% of quartets fully resolved. For Crowea, EA, eastern Australia; WA, western Australia." figureDoi="http://doi.org/10.5281/zenodo.13835486" httpUri="https://zenodo.org/record/13835486/files/figure.png" pageId="24" pageNumber="379">Fig. S5</figureCitation>
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).
|
||||
</paragraph>
|
||||
<paragraph id="6B5336FCE22BFF9B678FFCB4E96CFA2C" blockId="24.[98,770,180,1452]" pageId="24" pageNumber="379">
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|
|
@ -587,7 +590,7 @@ section
|
|||
‘Nigrostipulae’
|
||||
</emphasis>
|
||||
;
|
||||
<figureCitation id="F3D72A79E22BFF9B65BFFCD4E9BEFC0C" box="[690,762,884,908]" captionStart="Fig" captionStartId="17.[153,190,1812,1835]" captionTargetBox="[153,1434,185,1781]" captionTargetId="graphics-2@17.[153,1397,185,1755]" captionTargetPageId="17" captionText="Fig. 4. (Caption on next page)" pageId="24" pageNumber="379">Fig. 4</figureCitation>
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<figureCitation id="F3D72A79E22BFF9B65BFFCD4E9BEFC0C" box="[690,762,884,908]" captionStart="Fig" captionStartId="17.[153,190,1812,1835]" captionTargetBox="[153,1434,185,1781]" captionTargetId="graphics-2@17.[153,1397,185,1755]" captionTargetPageId="17" captionText="Fig. 4. (Caption on next page)" figureDoi="http://doi.org/10.5281/zenodo.13835479" httpUri="https://zenodo.org/record/13835479/files/figure.png" pageId="24" pageNumber="379">Fig. 4</figureCitation>
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, black square). In his revision of
|
||||
<taxonomicName id="ACEC4D7FE22BFF9B6513FC34EBF8FC4C" authority=", Wilson (1998 a)" authorityName=", Wilson" authorityYear="1998" class="Magnoliopsida" family="Rutaceae" genus="Eriostemon" kingdom="Plantae" order="Sapindales" pageId="24" pageNumber="379" phylum="Tracheophyta" rank="genus">
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<emphasis id="5998EAEEE22BFF9B6513FC34E9DCFC2C" bold="true" box="[542,664,916,940]" italics="true" pageId="24" pageNumber="379">Eriostemon</emphasis>
|
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|
|
|
|||
|
|
@ -1,68 +1,71 @@
|
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, contrasting support for monophyly (ptDNA;
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)
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), and that nrDNA sampling here (see the Supplementary ‘Methods and results’ section) and by
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@ -98,7 +101,7 @@ Duretto
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2023
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</bibRefCitation>
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). Even with this large dataset, we were unable to resolve backbone relationships between four supported major lineages of genera (
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<figureCitation id="F3D72A79E22BFF9B65A2F894E9B5F8CC" box="[687,753,1844,1868]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" pageId="24" pageNumber="379">Fig. 3</figureCitation>
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<figureCitation id="F3D72A79E22BFF9B65A2F894E9B5F8CC" box="[687,753,1844,1868]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" figureDoi="http://doi.org/10.5281/zenodo.13835473" httpUri="https://zenodo.org/record/13835473/files/figure.png" pageId="24" pageNumber="379">Fig. 3</figureCitation>
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). Across all analyses, these lineages were arranged on very short, unsupported branches that we have treated as a polytomy. Short divergences in molecular phylogenies may be explained by both biological and experimental causes. Biologically, polytomies can be the result of true multifurcations (so-called
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<emphasis id="5998EAEEE22BFF9B64E8FEB4EF5CFEAC" bold="true" box="[997,1048,276,300]" italics="true" pageId="24" pageNumber="379">hard</emphasis>
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polytomies) caused by rapid radiation and simultaneous divergence events. However, polytomies may arise as a result of reaching the limit of resolution in the estimated tree (so-called
|
||||
|
|
@ -163,14 +166,14 @@ Gonçalves
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|||
genes (
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<bibRefCitation id="0F7D4B0DE22BFF9B63B9F994EE73F9CC" author="Doyle JJ" box="[1204,1335,1588,1612]" pageId="24" pageNumber="379" pagination="476 - 489" refId="ref19830" refString="Doyle JJ (2021) Defining coalescent genes: theory meets practice in organelle phylogenomics. Systematic Biology 71, 476 - 489. doi: 10.1093 / sysbio / syab 053" type="journal article" year="2021">Doyle 2021</bibRefCitation>
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), rather than conflicting gene-tree topologies (this is also supported by gene discordance factors for the tree in
|
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<figureCitation id="F3D72A79E22BFF9B6209F9D4EE02F90C" box="[1284,1350,1652,1676]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" pageId="24" pageNumber="379">Fig. 3</figureCitation>
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<figureCitation id="F3D72A79E22BFF9B6209F9D4EE02F90C" box="[1284,1350,1652,1676]" captionStart="Fig" captionStartId="15.[164,201,1832,1855]" captionTargetBox="[98,1490,140,1802]" captionTargetId="graphics-2@15.[164,1280,193,1718]" captionTargetPageId="15" captionText="Fig. 3. (Caption on next page)" figureDoi="http://doi.org/10.5281/zenodo.13835473" httpUri="https://zenodo.org/record/13835473/files/figure.png" pageId="24" pageNumber="379">Fig. 3</figureCitation>
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||||
; mean gCF: 41.9, mean gDF1: 5.8, mean gDF2: 5.6 across all branches; see Data availability for file).
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</paragraph>
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<paragraph id="6B5336FCE22BFF9A645FF974EACFFEEC" blockId="24.[818,1491,180,1932]" lastBlockId="25.[98,770,180,1932]" lastPageId="25" lastPageNumber="380" pageId="24" pageNumber="379">
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||||
Second, we are able to dismiss noise caused by site saturation as a potential source of conflict on the basis of the persistence of the polytomy in the analyses of the likelihood mapping subsets (with noisy loci removed), the DNA alignment partitioned by codon position, and the translated
|
||||
<collectionCode id="0DFDAE39E22BFF9B643FF8D4E825F80C" box="[818,865,1908,1932]" country="Ecuador" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15840" lsid="urn:lsid:biocol.org:col:15840" name="Charles Darwin Research Station" pageId="24" pageNumber="379" type="Herbarium">CDS</collectionCode>
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alignment (Supplementary
|
||||
<figureCitation id="F3D72A79E22BFF9B63ABF8D4EFBEF80C" box="[1190,1274,1908,1932]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." pageId="24" pageNumber="379">Fig. S6</figureCitation>
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||||
<figureCitation id="F3D72A79E22BFF9B63ABF8D4EFBEF80C" box="[1190,1274,1908,1932]" captionStart="Fig" captionStartId="19.[311,348,1213,1236]" captionTargetBox="[198,1367,167,1182]" captionTargetId="graphics-304@19.[324,1275,284,732]" captionTargetPageId="19" captionText="Fig. 6. Results of topology tests for the backbone polytomy in the Eriostemon group. (a) The 15 possible resolutions of the polytomy (for the four supported clades) that testing was conducted on, ordered by most likely to least likely from left to right, top to bottom (note: the hard polytomy resolution is not depicted). (b) Plot of log likelihoods for each possible topology. The topology matching the most likely tree is denoted by a star, and the hard polytomy topology is denoted by a triangle." figureDoi="http://doi.org/10.5281/zenodo.13835488" httpUri="https://zenodo.org/record/13835488/files/figure.png" pageId="24" pageNumber="379">Fig. S6</figureCitation>
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||||
). Similarly, if rate variation among loci were a contributor of conflict, then our IQ-TREE analysis partitioned by locus would have produced a result different from that from the unpartitioned analysis. Hence, we consider it unlikely that conflicting phylogenetic signal is a significant cause of the short, unsupported branches of the polytomy.
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||||
</paragraph>
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||||
<paragraph id="6B5336FCE22AFF9A678FFED4E9EEFAEC" blockId="25.[98,770,180,1932]" pageId="25" pageNumber="380">
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