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142 results for “paraphyly”
Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation
<p>When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (<em>Zonotrichia atricapilla</em>) and the white-crowned sparrow (<em>Zonotrichia leucophrys</em>) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of <em>Z. leucophrys</em>. The two <em>Z. leucophrys</em> subspecies showed moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species <em>Z. leucophrys</em> and <em>Z. atricapilla</em> show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between <em>Z. atricapilla</em> and <em>Z. leucophrys</em> appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria appear highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing lack of gene flow between populations many hundreds of thousands of years before other genomic regions.</p>
Phylogenomics and Intergenomic Conflict in a Challenging Orchid Clade (Calypsoinae): Monophyly of Corallorhiza, Paraphyly of Oreorchis, and Resurrection of Kitigorchis
<p>Dataset S1: Concatenated nuclear sequence capture data (Angiosperms353) for Calypsoinae. This nexus file contains a partition block, which can be used to plit the data into individual alignments (in R, Trifusion, SequenceMatrix, etc.).</p> <p>Dataset S2: Concatenated nuclear sequence capture data (Angiosperms353) for Calypsoinae without partition block.</p> <p>Dataset S3: Concatenated mitochondrial sequence data for Calypsoinae.</p> <p>Dataset S4: Concatenated plastid gene sequence data for Calypsoinae.</p> <p> </p>
Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation
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Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.
Table 2 in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
<p><b>Table 2.</b> GenBank accession numbers for mitochondrion and <i>cytb</i> sequences used in analysis.</p><table><tbody><tr><th>Species</th><th>Mitochondrion</th><th>cytb</th></tr></tbody><tbody><tr><th><i>Glischropus aquilus</i></th><td></td><td>KR612333.1</td></tr><tr><th><i>G. bucephalus</i></th><td>OR667258</td><td>KR612331.1, KR612332.1, OR667259, OR667260, OR667261</td></tr><tr><th><i>G. tylopus</i></th><td></td><td>JX570898.1, EU521632.1, OR667262, OR667263</td></tr><tr><th><i>“</i> <i>Pipistrellus coromandra”</i></th><td>NC_029191.1</td><td>NC_029191.1</td></tr><tr><th><i>Nyctalus aviator</i></th><td>NC_060309.1</td><td>NC_060309.1, MK167360.1</td></tr><tr><th><i>N. labiata</i></th><td>NC_027237.1, NC_041160.1</td><td>NC_027237.1, NC_041160.1, KX467596.1</td></tr><tr><th><i>N. lasiopterus</i></th><td></td><td>DQ120867.1, EU360680.1, JX570900.1</td></tr><tr><th><i>N. leisleri</i></th><td></td><td>DQ120877.1, JX570901.1, EU360690.1</td></tr><tr><th><i>N. noctula</i></th><td>MN122876.1, MN122907.1</td><td>MN122907.1, MN122876.1, DQ120872.1</td></tr><tr><th><i>Pipistrellus abramus</i></th><td>KX355640.1, NC_005436.1</td><td>GQ332529.1, KX355640.1, NC_005436.1</td></tr><tr><th><i>P. deserti</i></th><td></td><td>KM252759.1</td></tr><tr><th><i>P. coromandra</i></th><td></td><td>OR667264, OR667265, OR667266, OR667267</td></tr><tr><th><i>P. dhofarensis</i></th><td></td><td>KX375145.1, KX375148.1</td></tr><tr><th><i>P. hesperidus</i></th><td></td><td>MN790830.1, MT778037.1, MN790820.1</td></tr><tr><th><i>P. javanicus</i></th><td></td><td>KX496357.1</td></tr><tr><th><i>P. kuhlii</i></th><td>KU058655.1</td><td>KU058655.1, DQ120845.1, EU360657.1</td></tr><tr><th><i>P. maderensis</i></th><td></td><td>KC520771.1, KC520774.1, MT374272.1</td></tr><tr><th><i>P. nanulus</i></th><td></td><td>MK188530.1</td></tr><tr><th><i>P. nathusii</i></th><td>MN122914.1</td><td>MN122914.1, AJ504446.1, DQ120849.1</td></tr><tr><th><i>P. paterculus</i></th><td></td><td>OR667268, OR667269, OR667270</td></tr><tr><th><i>P. pipistrellus</i></th><td>LR862378.1</td><td>KF874520.1, DQ120853.1, LR862378.1</td></tr><tr><th><i>P. pygmaeus</i></th><td>MN122927.1, OX465325.1</td><td>MN122927.1, OX465325.1, EU084882.1</td></tr><tr><th><i>P. raceyi</i></th><td></td><td>KM886094.1, KM886088.1</td></tr><tr><th><i>P. rusticus</i></th><td></td><td>KX375166.1, KX375167.1</td></tr><tr><th><i>P. stenopterus</i></th><td></td><td>MH540194.1</td></tr><tr><th><i>Plecotus auritus</i></th><td>MN122881.1, MT410875.1</td><td></td></tr><tr><th><i>P. macrobullaris</i></th><td>KR134372.1, KR134385.1</td><td></td></tr><tr><th><i>Hypsugo alaschanicus</i></th><td>MF459671.1, MK135784.1, NC_029939.1</td><td></td></tr><tr><th><i>Lasionycteris noctivagans</i></th><td>MT774150.1, MT774151.1, NC_050995.1</td><td></td></tr><tr><th><i>Chalinolobus tuberculatus</i></th><td>NC 002626.1</td><td></td></tr><tr><th><i>Eptesicus bottae</i></th><td>NC_070014.1, OP328299.1, OP328300.1</td><td></td></tr><tr><th><i>E. nilssonii</i></th><td>OX621305.1</td><td></td></tr><tr><th><i>Vespertilio murinus</i></th><td>NC_033347.1</td><td>NC_033347.1</td></tr><tr><th><i>V. sinensis</i></th><td>KJ081440.1, KM092493.1.</td><td>KJ081440.1, KM092493.1.</td></tr><tr><th><i>Myotis brandtii</i></th><td>NC_025308.1</td><td></td></tr><tr><th><i>M. horsfieldii</i></th><td>MF143494.1</td><td></td></tr><tr><th><i>M. muricola</i></th><td>KT213444.1</td><td></td></tr></tbody></table>
Table 3 in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
<p><b>Table 3.</b> Gene organization and characterization of the <i>G. bucephalus</i> mitogenome.</p><table><tbody><tr><th></th><th><b>Start Position</b></th><th><b>Stop Position</b></th><th><b>Length (bp)</b></th><th><b>Anticodon</b></th><th><b>Start Codon</b></th><th><b>Stop Codon</b></th><th><b>Strand</b></th></tr></tbody><tbody><tr><th>tRNAPhe</th><td>1</td><td>73</td><td>73</td><td>GAA</td><td></td><td></td><td>+</td></tr><tr><th>12S rRNA</th><td>74</td><td>1010</td><td>937</td><td></td><td></td><td></td><td>+</td></tr><tr><th>tRNAVal</th><td>1011</td><td>1078</td><td>68</td><td>TAC</td><td></td><td></td><td>+</td></tr><tr><th>16S rRNA</th><td>1079</td><td>2644</td><td>1566</td><td></td><td></td><td></td><td>+</td></tr><tr><th>tRNALeu</th><td>2650</td><td>2725</td><td>76</td><td>TAA</td><td></td><td></td><td>+</td></tr><tr><th>Nd1</th><td>2731</td><td>3684</td><td>954</td><td></td><td>ATG</td><td>TA-</td><td>+</td></tr><tr><th>tRNAIle</th><td>3687</td><td>3755</td><td>69</td><td>GAT</td><td></td><td></td><td>+</td></tr><tr><th>tRNAGln</th><td>3753</td><td>3827</td><td>75</td><td>TTG</td><td></td><td></td><td>-</td></tr><tr><th>tRNAMet</th><td>3828</td><td>3896</td><td>69</td><td>CAT</td><td></td><td></td><td>+</td></tr><tr><th>Nd2</th><td>3897</td><td>4937</td><td>1041</td><td></td><td>ATT</td><td>T-</td><td>+</td></tr><tr><th>tRNATrp</th><td>4939</td><td>5005</td><td>67</td><td>TCA</td><td></td><td></td><td>+</td></tr><tr><th>tRNAAla</th><td>5013</td><td>5081</td><td>69</td><td>TGC</td><td></td><td></td><td>-</td></tr><tr><th>tRNAAsn</th><td>5082</td><td>5154</td><td>73</td><td>GTT</td><td></td><td></td><td>-</td></tr><tr><th>OR</th><td>5155</td><td>5189</td><td>35</td><td></td><td></td><td></td><td></td></tr><tr><th>tRNACys</th><td>5187</td><td>5252</td><td>66</td><td>GCA</td><td></td><td></td><td>-</td></tr><tr><th>tRNATyr</th><td>5253</td><td>5319</td><td>67</td><td>GTA</td><td></td><td></td><td>-</td></tr><tr><th>Cox1</th><td>5321</td><td>6862</td><td>1542</td><td></td><td>ATG</td><td>TAA</td><td>+</td></tr><tr><th>tRNASer</th><td>6869</td><td>6937</td><td>69</td><td>TGA</td><td></td><td></td><td>-</td></tr><tr><th>tRNAAsp</th><td>6945</td><td>7011</td><td>67</td><td>GTC</td><td></td><td></td><td>+</td></tr><tr><th>Cox2</th><td>7012</td><td>7692</td><td>681</td><td></td><td>ATG</td><td>TAA</td><td>+</td></tr><tr><th>tRNALys</th><td>7699</td><td>7765</td><td>67</td><td>TTT</td><td></td><td></td><td>+</td></tr><tr><th>ATP8</th><td>7767</td><td>7967</td><td>201</td><td></td><td>ATG</td><td>TAA</td><td>+</td></tr><tr><th>ATP6</th><td>7928</td><td>8605</td><td>678</td><td></td><td>ATG</td><td>TAA</td><td>+</td></tr><tr><th>Cox3</th><td>8608</td><td>9390</td><td>783</td><td></td><td>ATG</td><td>TA-</td><td>+</td></tr><tr><th>tRNAGly</th><td>9392</td><td>9460</td><td>69</td><td>TCC</td><td></td><td></td><td>+</td></tr><tr><th>Nd3</th><td>9461</td><td>9805</td><td>345</td><td></td><td>ATT</td><td>TA-</td><td>+</td></tr><tr><th>tRNAArg</th><td>9809</td><td>9878</td><td>70</td><td>TCG</td><td></td><td></td><td>+</td></tr><tr><th>Nd4L</th><td>9880</td><td>10,173</td><td>294</td><td></td><td>ATG</td><td>TAA</td><td>+</td></tr><tr><th>Nd4</th><td>10,170</td><td>11,546</td><td>1377</td><td></td><td>ATG</td><td>T-</td><td>+</td></tr><tr><th>tRNAHis</th><td>11,548</td><td>11,616</td><td>69</td><td>GTG</td><td></td><td></td><td>+</td></tr><tr><th>tRNASer</th><td>11,617</td><td>11,675</td><td>59</td><td>GCT</td><td></td><td></td><td>+</td></tr><tr><th>tRNALeu</th><td>11,676</td><td>11,745</td><td>70</td><td>TAG</td><td></td><td></td><td>+</td></tr><tr><th>Nd5</th><td>11,764</td><td>13,552</td><td>1789</td><td></td><td>ATA</td><td>TAA</td><td>+</td></tr><tr><th>Nd6</th><td>13,544</td><td>14,062</td><td>519</td><td></td><td>ATG</td><td>TAA</td><td>-</td></tr><tr><th>tRNAGlu</th><td>14,066</td><td>14,133</td><td>68</td><td>TTC</td><td></td><td></td><td>-</td></tr><tr><th>CytB</th><td>14,139</td><td>15,275</td><td>1137</td><td></td><td>ATG</td><td>AGA</td><td>+</td></tr><tr><th>tRNAThr</th><td>15,279</td><td>15,348</td><td>70</td><td>TGT</td><td></td><td></td><td>+</td></tr><tr><th>tRNAPro</th><td>15,348</td><td>15,416</td><td>69</td><td>TGG</td><td></td><td></td><td>-</td></tr><tr><th>D-loop</th><td>15,416</td><td>17,023</td><td>1608</td><td></td><td></td><td></td><td></td></tr></tbody></table>
Table 1 in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
<p><b>Table 1.</b> Model types for protein-coding gene analysis configured by IQtree ModelFinder through ultrafast bootstrap (10,000 replicates) for the phylogenetic tree with 3 codons.</p><table><tbody><tr><th>Model Type</th><th></th><th></th><th></th><th></th><th></th><th></th><th>Gene</th><th></th><th></th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th></th><td>ND1</td><td>ND2</td><td>COX1</td><td>COX2</td><td>ATP8</td><td>ATP6</td><td>COX3</td><td>ND3</td><td>ND4L</td><td>ND4</td><td>ND5</td><td>ND6</td><td>CYTB</td></tr><tr><th>GTR+F+G4</th><td>1st pos</td><td></td><td></td><td>1st pos</td><td></td><td>1st pos</td><td></td><td>1st pos</td><td></td><td></td><td></td><td></td><td>1st pos</td></tr><tr><th>TPM3u+F+I+G4</th><td>2nd pos</td><td></td><td>2nd pos</td><td>2nd pos</td><td></td><td>2nd pos</td><td>2nd pos</td><td></td><td></td><td></td><td></td><td></td><td>2rd pos</td></tr><tr><th>TIM+F+I+G4</th><td>3rd pos</td><td>3rd pos</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>3rd pos</td></tr><tr><th>TIM2+F+I+G4</th><td></td><td>1st pos</td><td></td><td></td><td>1st pos, 2nd pos</td><td></td><td></td><td></td><td>1st pos</td><td>1st pos</td><td>1st pos</td><td></td><td></td></tr><tr><th>TPM3u+F+I+G4</th><td></td><td>2nd pos</td><td></td><td></td><td></td><td></td><td></td><td>2nd pos</td><td>2nd pos</td><td>2nd pos</td><td>2nd pos</td><td></td><td></td></tr><tr><th>TIM2e+I+G4</th><td></td><td></td><td>1st pos</td><td></td><td></td><td></td><td>1st pos</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>TIM2+F+I+G4</th><td></td><td></td><td>3rd pos</td><td>3rd pos</td><td>3rd pos</td><td>3rd pos</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>TN+F+I+G4</th><td></td><td></td><td></td><td></td><td></td><td></td><td>3rd pos</td><td>3rd pos</td><td>3rd pos</td><td>3rd pos</td><td>3rd pos</td><td></td><td></td></tr><tr><th>HKY+F+I+G4</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>1st pos, 2nd pos</td><td></td></tr><tr><th>HKY+F+G4</th><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>3rd pos</td><td></td></tr></tbody></table>
TABLE 1 TABLE 2 in Polybia, Paraphyly, and Polistine Phylogeny
<p>TABLE 1 <b>Adult Characters for Subgenera of <i>Polybia</i> and</b> <b>Five Outgroup Genera</b> Multistate character 15 is treated as additive; multistate characters are otherwise treated as nonadditive. An asterisk denotes a polymorphism showing all applicable states; a dollar sign denotes a subset polymorphism (<i>Myrapetra</i>: states 0 and 1 in character 1, 0 and 1 in character 11, and 1 and 4 in character 20; and <i>Trichinothorax</i>: states 0 and 2 in character 1, 0 and 1 in character 5, 0 and 1 in character 11, 0 and 1 in character 14, 1 and 3 in character 20, and 0 and 1 in character 23).</p><table><tbody><tr><th>Taxa</th><th>Character</th></tr><tr><th>1 5 10 15 20 | | | | |</th></tr></tbody><tbody><tr><th><i>Protonectarina</i></th><td>200020001000020100000002</td></tr><tr><th><i>Epipona</i></th><td>002021011011120000052000</td></tr><tr><th><i>Synoecoides</i></th><td>011120110000102002131031</td></tr><tr><th><i>Chartergus</i></th><td>000000000001000103260012</td></tr><tr><th><i>Brachygastra</i></th><td>2000$0000001000103261012</td></tr><tr><th><i>Polybia</i></th><td>010100100020101001130013</td></tr><tr><th><i>Apopolybia</i></th><td>010100100000111011121023</td></tr><tr><th><i>Alpha</i></th><td>010100100000111001020013</td></tr><tr><th><i>Myrapetra</i></th><td>$10000**00$01100000$0004</td></tr><tr><th><i>Furnariana</i></th><td>01010000010*100101011024</td></tr><tr><th><i>Cylindroeca</i></th><td>010111011220100100001014</td></tr><tr><th><i>Trichinothorax</i></th><td>$10*$10**0$01$01*00$10$4</td></tr><tr><th><i>Pedothoeca</i></th><td>010121011010110100000024</td></tr><tr><th><i>Formicicola</i></th><td>010100110000111101020124</td></tr><tr><th><i>Platypolybia</i></th><td>110110110000120101010024</td></tr></tbody></table>
TABLE 3 in Polybia, Paraphyly, and Polistine Phylogeny
<p>TABLE 3 <b>Nest Characters for Subgenera of <i>Polybia</i>, and Five Outgroup Genera</b> Multistate characters are treated as nonadditive. The question mark denotes a missing value. An asterisk denotes a polymorphism showing all applicable states.</p><table><tbody><tr><th>Taxa</th><th>Character</th></tr><tr><th>46 50 | |</th></tr></tbody><tbody><tr><th><i>Protonectarina</i></th><td>031100000</td></tr><tr><th><i>Epipona</i></th><td>000100101</td></tr><tr><th><i>Synoecoides</i></th><td>000011101</td></tr><tr><th><i>Chartergus</i></th><td>030100011</td></tr><tr><th><i>Brachygastra</i></th><td>010011110</td></tr><tr><th><i>Polybia</i></th><td>100000001</td></tr><tr><th><i>Apopolybia</i></th><td>100010000</td></tr><tr><th><i>Alpha</i></th><td>111001101</td></tr><tr><th><i>Furnariana</i></th><td>020000111</td></tr><tr><th><i>Cylindroeca</i></th><td>10001?100</td></tr><tr><th><i>Trichinothorax</i></th><td>001210100</td></tr><tr><th><i>Pedothoeca</i></th><td>020010100</td></tr><tr><th><i>Formicicola</i></th><td>000100100</td></tr><tr><th><i>Myrapetra</i></th><td>*00010***</td></tr><tr><th><i>Platypolybia</i></th><td>000010011</td></tr></tbody></table>
TABLE 2 in Polybia, Paraphyly, and Polistine Phylogeny
<p>TABLE 2 <b>Larval Characters for Subgenera of <i>Polybia</i>,</b> <b>and Five Outgroup Genera</b> Multistate characters are treated as nonadditive. Question marks denote missing values; the larva of the genus <i>Synoecoides</i> and of the subgenera <i>Furnariana</i> and <i>Platypolybia</i>, are unknown. An asterisk denotes a polymorphism showing all applicable states; a dollar sign denotes a subset polymorphism (<i>Chartergus</i>: states 0 and 1 in character 41; <i>Brachygastra</i>: states 0 and 1 in character 37; <i>Myraptetra</i>: states 1 and 2 in character 41; and <i>Trichinothorax</i>: states 1 and 2 in character 35, and 0 and 2 in character 37).</p><table><tbody><tr><th>Taxa</th><th>Character</th></tr><tr><th>25 29 34 39 44 | | | | |</th></tr></tbody><tbody><tr><th><i>Protonectarina</i></th><td>0?1110???200??0??0???</td></tr><tr><th><i>Epipona</i></th><td>0100011-1210100010110</td></tr><tr><th><i>Synoecoides</i></th><td>?????????????????????</td></tr><tr><th><i>Chartergus</i></th><td>0011110102201100$0001</td></tr><tr><th><i>Brachygastra</i></th><td>011101*00321$10*10000</td></tr><tr><th><i>Polybia</i></th><td>?011?1010210000010001</td></tr><tr><th><i>Apopolybia</i></th><td>001111???01???0??????</td></tr><tr><th><i>Alpha</i></th><td>0011011-0100010010001</td></tr><tr><th><i>Myrapetra</i></th><td>*011*1*1*2200**0$0001</td></tr><tr><th><i>Furnariana</i></th><td>?????????????????????</td></tr><tr><th><i>Cylindroeca</i></th><td>?0??11???01???0??????</td></tr><tr><th><i>Trichinothorax</i></th><td>1011111-00$0$00010001</td></tr><tr><th><i>Pedothoeca</i></th><td>001111*1132101001*00*</td></tr><tr><th><i>Formicicola</i></th><td>10110101022100001100?</td></tr><tr><th><i>Platypolybia</i></th><td>?????????????????????</td></tr></tbody></table>
Arthropod mtDNA paraphyly: a case study of introgressive origin
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Data for: Unraveling the evolution of mycetophagy and phytophagy in fungus weevils (Curculionoidea: Anthribidae): phylogenomic insights into Anthribinae paraphyly and tribal non-monophyly
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Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
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Extensive paraphyly in the typical owl family (Strigidae)
<p>The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera <i>Athene</i>, <i>Otus</i>, <i>Asio</i>, <i>Megascops, Bubo</i>, and <i>Strix </i>are<i> </i>paraphyletic, whereas <i>Ninox</i> and <i>Glaucidium</i> are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions.</p>
Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)
Species-level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. The present study aims to test the underlying causes behind the observed paraphyly of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (P. musicus), but nuclear genealogies support a sister-group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto-nuclear incongruence. Further Approximate Bayesian Computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene-tree paraphyly.
Data from: Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)
The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier & Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753 bp) and cytochrome b (CytB, 587 bp) mitochondrial genes, and the nuclear ribosomal internal transcribed spacer 2 (ITS2, 426 bp). The combination of mitochondrial and nuclear data strongly supports the paraphyly of the genus Stomoxys because of the inclusion of Prostomoxys saegerae Zumpt. This unexpected result suggests that Prostomoxys should be renamed into Stomoxys. Also, the deep molecular divergence observed between the subspecies Stomoxys niger niger Macquart and S. niger bilineatus Grünbreg led us to propose that they should rather be considered as distinct species, in agreement with ecological data. Bayesian phylogenetic analyses support three distinct lineages within the genus Stomoxys with a strong biogeographical component. The first lineage consists solely of the divergent Asian species S. indicus Picard which appears as the sister-group to all remaining Stomoxys species. The second clade groups the strictly African species Stomoxys inornatus Grünbreg, Stomoxys transvittatus Villeneuve, Stomoxys omega Newstead, and Stomoxys pallidus Roubaud. Finally, the third clade includes both African occurring and more widespread species such as the livestock pest Stomoxys calcitrans Linnaeus. Divergence time estimates indicate that the genus Stomoxys originated in the late Oligocene around 30 million years ago, with the major lineages diversifying in the Early Miocene between 20 and 15 million years ago at a time when temperate forests developed in the Northern Hemisphere.
FIGURE 4 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 4. Dorsal and ventral views of preserved (A) male holotype of Hyperolius veithi sp. nov. (photos by F. Feß), SVL 26.3 mm, (B) female holotype of Hyperolius schoutedeni (photos by MRAC, through the courtesy of D. Meirte), SVL 26.4 mm.
FIGURE 3 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 3. Bayesian phylogram of Hyperolius species including Cinnamon-belly reed frogs inferred from nucleotide sequence data from 16S mitochondrial rRNA. Bayesian posterior probabilities> 0.95 each are marked by an asterisk on branch. We here apply species names as given in Table 1; in the Cinnamon-belly reed frog clade, numbers in parentheses give sample size of the same haplotype, which corresponds with localities. Note that Hyperolius cinnamomeoventris is paraphyletic. Topotypic material of H. olivaceus (#) and H. cinnamomeoventris (##) are indicated. Hyperolius sp. 'Salonga' is H. veithi sp. nov. Both the Hierarchical Likelihood Ratio Tests and Akaike Information Criterion implemented in MrModeltest selected a GTR+I+G model with a gamma distribution of 0.5912 and a proportion of invariable sites of 0.2291 (estimated base frequencies: A: 0.3294, C: 0.2260, G: 0.1813, T: 0.2633; rate matrix: A-C: 3.0708, A-G: 7.4382, A-T: 5.3616, C-G: 1.5864, C-T: 21.7283, G-T: 1.0000).
FIGURE 1 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 1. Map of Central Africa and adjacent areas showing Salonga National Park (white contour line), distribution of H. cinnamomeoventris according to the IUCN Red List (http://www.iucnredlist.org) following the 2002 2004 IUCN Global Amphibian Assessment (bold black contour line) and localities of our genetic sampling from type localities (reverse filled triangle—H. cinnamomeoventris and H. tristis, white circle—H. veithi sp. nov., filled square—H. ituriensis, filled triangle— H. olivaceus and H. fimbriolatus) and additional localities (small filled dots). In addition, the type locality of H. wittei (cross) is shown. Note that H. veithi syntopically occurs with H. cinnamomeoventris.
FIGURE 2 in New species of reed frog from the Congo basin with discussion of paraphyly in Cinnamon-belly reed frogs
FIGURE 2. Life aspects of: (A) Hyperolius veithi sp. nov. in amplexus (unidentified paratypes; photo J. Kielgast), note that there is a yellow spot on the heel visible in the male frog; (B) H. cinnamomeoventris male in PhJ from the type locality (AC 3008; photo A. Channing); (C) H. cinnamomeoventris female from the Kakamega Forest, Kenya (not collected; photo S. Lötters); (D) H. cinnamomeoventris male in PhJ from Semliki, Uganda (SL 555; photo A. Channing); (E) H. molleri from São Tomé (photo D. Lin, CAS) and (F) H. thomensis from São Tomé in amplexus (photo D. Lin, CAS).
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Annotated Behaviour and Observability Dataset (ABODe)
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