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389 results for “ancestral”
Data from: Sexually antagonistic genetic variance for fitness in an ancestral and a novel environment
The intersex genetic correlation for fitness (rwfm), a standardized measure of the degree to which male and female fitness covary genetically, has consequences for important evolutionary processes, but few estimates are available and none have explored how it changes with environment. Using a half-sibling breeding design, we estimated the genetic (co)variance matrix (G) for male and female fitness, and the resulting rwfm,in Drosophila serrata. Our estimates were performed in two environments: the laboratory yeast food to which the population was well adapted and a novel corn food. The major axis of genetic variation for fitness in the two environments, accounting for 51.3 per cent of the total genetic variation, was significant and revealed a strong signal of sexual antagonism, loading negatively in both environments on males but positively on females. Consequently, estimates of rwfm were negative in both environments (-0.34 and -0.73, respectively), indicating that the majority of genetic variance segregating in this population has contrasting effects on male and female fitness. The possible strengthening of the negative rwfm in this novel environment may be a consequence of no history of selection for amelioration of sexual conflict. Additional studies from a diverse range of novel environments will be needed to determine the generality of this finding.
Data from: microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate
Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more primitive microRNA families, and 22 unique substitutions to the mature gene products. Reanalysis of morphological data reveals that support for cyclostome paraphyly was based largely on incorrect character coding, and a revised dataset is not decisive on the mono- vs. paraphyly of cyclostomes. Furthermore, we show fundamental conservation of microRNA expression patterns among lamprey, hagfish, and gnathostome organs, implying that the role of microRNAs within specific organs is coincident with their appearance within the genome and is conserved through time. Together, these data support the monophyly of cyclostomes and suggest that the last common ancestor of all living vertebrates was a more complex organism than conventionally accepted by comparative morphologists and developmental biologists.
Data from: Quantitative genetics of female mate preferences in an ancestral and a novel environment
A female's mate preference is a potentially complex function relating variation in multiple male phenotypes with her probability of accepting individual males as a mate. Estimating the quantitative genetic basis of preference functions within a population is empirically challenging yet key to understanding preference evolution. We employed a recently described approach that uses random-coefficient mixed models in the analysis of function-valued traits. Using a half-sibling breeding design in a laboratory-adapted Drosophila serrata population, we estimated the genetic (co)variance function of female preference for male sexual displays composed of nine contact pheromones. The breeding design was performed across two environments: the food to which the population was well adapted and a novel food that reduced average female productivity by 35%. Significant genetic variance in female preference was detected and the majority (64.2%) was attributable to a single genetic dimension (eigenfunction), suggesting that preferences for different pheromones are not genetically independent. The second eigenfunction, accounting for 24% of the total genetic variance, approached significance in a conservative test, suggesting the existence of a second, independent genetic dimension. There was no evidence that the genetic basis of female preference differed between the two environments, suggesting the absence of genotype-by-environment interactions and hence a lack of condition-dependent preference expression.
Data from: Palaeohistological evidence for ancestral high metabolic rate in archosaurs
Metabolic heat production in archosaurs has played an important role in their evolutionary radiation during the Mesozoic, and their ancestral metabolic condition has long been a matter of debate in systematics and palaeontology. The study of fossil bone histology provides crucial information on bone growth rate, which has been used to indirectly investigate the evolution of thermometabolism in archosaurs. However, no quantitative estimation of metabolic rate has ever been performed on fossils using bone histological features. Moreover, to date, no inference model has included phylogenetic information in the form of predictive variables. Here we performed statistical predictive modelling using the new method of phylogenetic eigenvector maps on a set of bone histological features for a sample of extant and extinct vertebrates, in order to estimate metabolic rates of fossil archosauromorphs. This modelling procedure serves as a case study for eigenvector-based predictive modelling in a phylogenetic context, as well as an investigation of the poorly known evolutionary patterns of metabolic rate in archosaurs. Our results show that Mesozoic theropod dinosaurs exhibit metabolic rates very close to those found in modern birds, that archosaurs share an higher ancestral metabolic rate than that of extant ectotherms, and that this derived high metabolic rate was acquired at a much more inclusive level of the phylogenetic tree, among non-archosaurian archosauromorphs. These results also highlight the difficulties of assigning a given heat production strategy (i.e. endothermy, ectothermy) to an estimated metabolic rate value, and confirm findings of previous studies that the definition of the endotherm/ectotherm dichotomy may be ambiguous.
Figure 1 from: Vázquez-López M, Ramírez-Barrera SM, Terrones-Ramírez AK, Robles-Bello SM, Nieto-Montes de Oca A, Ruegg K, Hernández-Baños BE (2024) Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis. ZooKeys 1188: 169-195. https://doi.org/10.3897/zookeys.1188.107047
Figure 1 Maximum likelihood phylogeny with nextRAD data for Euphoniinae. A1, A2: genus Chlorophonia, B1, B2, and B3 genus Euphonia. From top to bottom, the illustrations depict AC. occipitalisBC. elegantissimaCE. jamaicaDE. luteicapillaEE. pectoralisFE. anneaeGE. hirundinacea. The illustrations were created by Germán García Lugo.
Figure 4 from: Vázquez-López M, Ramírez-Barrera SM, Terrones-Ramírez AK, Robles-Bello SM, Nieto-Montes de Oca A, Ruegg K, Hernández-Baños BE (2024) Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis. ZooKeys 1188: 169-195. https://doi.org/10.3897/zookeys.1188.107047
Figure 4 Biogeographical ancestral area reconstruction from BioGeoBEARS. Time Calibrated Tree with hypothetical ancestral areas and present areas and Biogeographical areas used in this study. The areas were mapped using ArcGIS (ArcMAP 10.2.2; Esri, Redlands, CA, USA) and the Biogeographic Regionalization on the Neotropical region shapefiles (Löwenberg 2014; Morrone 2014) see the text for more information.
Figure 2 from: Vázquez-López M, Ramírez-Barrera SM, Terrones-Ramírez AK, Robles-Bello SM, Nieto-Montes de Oca A, Ruegg K, Hernández-Baños BE (2024) Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis. ZooKeys 1188: 169-195. https://doi.org/10.3897/zookeys.1188.107047
Figure 2 Maximum likelihood phylogeny based on ND2 data for Euphoniinae. A1 and A2: genus Chlorophonia, B1, B2, and B3 genus Euphonia.
Supplementary material 1 from: Vázquez-López M, Ramírez-Barrera SM, Terrones-Ramírez AK, Robles-Bello SM, Nieto-Montes de Oca A, Ruegg K, Hernández-Baños BE (2024) Biogeographic factors contributing to the diversification of Euphoniinae (Aves, Passeriformes, Fringillidae): a phylogenetic and ancestral areas analysis. ZooKeys 1188: 169-195. https://doi.org/10.3897/zookeys.1188.107047
Supplementary information
Dataset:Ancestral Bright Spots: revealing the transformative potential of Indigenous and Local Communities' initiatives
Open the record for dataset details and reuse information.
FIGURE. 3a in Molecular investigation of the intra-specific genetic variation in Plantago ovata Forssk. (Plantaginaceae): An insight into potential ancestral area distribution and probable time of dispersal versus vicariance events
FIGURE. 3a: Brownish midrib of the bract; b: reddish-brown midrib on the corolla lobes in P. ovata.
Supplementary material 3 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Table S1: Explanation note: Species included in the present study.
Supplementary material 1 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Fig. S1:
Supplementary material 2 from: Roxo FF, Ochoa LE, Silva GSC, Oliveira C (2015) Rhinolekos capetinga: a new cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments on its ancestral dispersal route. ZooKeys 481: 109-130. https://doi.org/10.3897/zookeys.481.8755
Fig. S2:
Figure 1 in Abundance And Distribution Of The Philippine Brown Deer (Rusa Marianna Desmarest, 1822) In The Obu Manuvu Ancestral Domain, Mindanao Island, Philippines
Figure 1. Map of the study area in the Obu Manuvu Ancestral Domain, Mindanao Island, Davao City. (Cartographers: Ricksterlie C. Verzosa and Shunjay L. Abordo).
Figure 3 in Abundance And Distribution Of The Philippine Brown Deer (Rusa Marianna Desmarest, 1822) In The Obu Manuvu Ancestral Domain, Mindanao Island, Philippines
Figure 3. Location of the ten (10) camera trap stations in (A) Barangay Carmen, (B) Salaysay, (C) Tambobong, and (D) Tawan-tawan in the Obu Manuvu Ancestral Domain, Davao City, Philippines.
Figure 3 in Abundance And Distribution Of The Philippine Brown Deer (Rusa Marianna Desmarest, 1822) In The Obu Manuvu Ancestral Domain, Mindanao Island, Philippines
Figure 3. Location of the ten (10) camera trap stations in (A) Barangay Carmen, (B) Salaysay, (C) Tambobong, and (D) Tawan-tawan in the Obu Manuvu Ancestral Domain, Davao City, Philippines.
Fig. 2 in Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty
Fig. 2 Novelty in ancestral genomes. a Proportion of Novel HG in the Ancestral HG for different holozoan ancestors. b Percentage of Core HG that are novel, and percentage of highly preserved genes among the Novel HG across different LCA. c Number of Protein Class GO hits for the fruit fly representatives of the Novel HG for the various phylogenetic nodes
Benchmarking tree and ancestral sequence inference for B cell receptor sequences
<p>Simulation data used and described in associated article.</p>
Table 4. Molecular dating and ancestral area reconstruction results for Liphistius using S in Molecular phylogeny, biogeography, and species delimitation of segmented spider genus Liphistius (Araneae: Liphistiidae) in Thailand
<p><b>Table 4.</b> Molecular dating and ancestral area reconstruction results for <i>Liphistius</i> using S-DIVALIKE+J. The letters A–I correspond to geographical locations shown in Figure 4. The notation shows the biogeographic event in the phylogenetic tree (Fig. 4A) includes →: from the parent node to descendent nodes; ^: Sympatric speciation; |: Vicariance.</p><table><tbody><tr><th><b>Diversification events</b></th><th><b>Dates</b></th><th><b>DIVALIKE+J</b></th><th></th><th></th></tr><tr><th></th><th><b>(Mya)</b></th><th><b>Ancestral areas</b></th><th><b>Process</b></th><th><b>Route and probability</b></th></tr></tbody><tbody><tr><th>The most recent common ancestor of Liphistiidae</th><td>100</td><td>BCI 13.60</td><td>Dispersal:0</td><td>BCI→I|BC</td></tr><tr><th>(Fig. 4, number 1)</th><td></td><td>CEI 13.33</td><td>Vicariance:1</td><td>prob:.02</td></tr><tr><th></th><td></td><td>BEI 10.96</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Heptathelinae</th><td>58.43</td><td>I 100</td><td>Dispersal:0</td><td>I→I^I→I| I</td></tr><tr><th></th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>Liphistius</i></th><td>53.61</td><td>BC 14.34</td><td>Dispersal:0</td><td>BC→C|B</td></tr><tr><th>(Fig. 4, number 2)</th><td></td><td>CE 14.05</td><td>Vicariance:1</td><td>prob:.03</td></tr><tr><th></th><td></td><td>C 12.37</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>L. indra</i> + <i>L.</i></th><td>45.51</td><td>C 45.23</td><td>Dispersal:1</td><td>C→CE→C|E</td></tr><tr><th><i>lahu</i> (Fig. 4, number 3)</th><td></td><td>E 38.20</td><td>Vicariance:1</td><td>prob:.45</td></tr><tr><th></th><td></td><td>CE 16.50</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>trang</i> species</th><td>49.61</td><td>B 39.38</td><td>Dispersal:1</td><td>B→DB→D|B</td></tr><tr><th>group + <i>bristowei</i> species group (Fig. 3, number 4)</th><td></td><td>D 30.43</td><td>Vicariance:1</td><td>prob:.30</td></tr><tr><th></th><td></td><td>BD 14.72</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>bristowei</i> spe-</th><td>32.86</td><td>D 75.76</td><td>Dispersal:0</td><td>D→D^D→D|D</td></tr><tr><th>cies group (Fig. 4, number 5)</th><td></td><td>C 21.28</td><td>Vicariance:0</td><td>prob:.55</td></tr><tr><th></th><td></td><td>A 2.02</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>trang</i> species</th><td>46.54</td><td>B 99.88</td><td>Dispersal:0</td><td>B→B^B→B| B</td></tr><tr><th>group (Fig. 4, number 6)</th><td></td><td>A 0.08</td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td>H 0.01</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Sibumasu I</th><td>41.39</td><td>B 100</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>clade (Fig. 4, number 7)</th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Sinbumasu II–</th><td>42.48</td><td>B 99.76</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>IV and Indochina clades (Fig. 4, number 8)</th><td></td><td>A 0.18</td><td>Vicariance:0</td><td>prob:.96</td></tr><tr><th></th><td></td><td>G 0.03</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu II</th><td>30.56</td><td>B 99.91</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>(Fig. 4, number 9)</th><td></td><td>A 0.09</td><td>Vicariance:0</td><td>prob:.97</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu</th><td>38.89</td><td>B 96.03</td><td>Dispersal:1</td><td>B→AB→A|B</td></tr><tr><th>III–IV and Indochina clade (Fig. 4, number 10)</th><td></td><td>A 2.65</td><td>Vicariance:1</td><td>prob:.48</td></tr><tr><th></th><td></td><td>G 0.67</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu III</th><td>31.69</td><td>A 51.95</td><td>Dispersal:0</td><td>A→A^A→A| A</td></tr><tr><th>(Fig. 4, number 11)</th><td></td><td>B 48.05</td><td>Vicariance:0</td><td>prob:.26</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu</th><td>34.81</td><td>B 96.15</td><td>Dispersal:1</td><td>B→BG→B| G</td></tr><tr><th>IV + Indochina clade (Fig. 4, number 12)</th><td></td><td>G 1.94</td><td>Vicariance:1</td><td>prob:.48</td></tr><tr><th></th><td></td><td>H 1.90</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu IV</th><td>17.02</td><td>B 100</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>(Fig. 4, number 13)</th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Indochina</th><td>31.15</td><td>G 50.43</td><td>Dispersal:1</td><td>G→GH→G|H</td></tr><tr><th>clade (Fig. 4, number 14)</th><td></td><td>H 49.38</td><td>Vicariance:1</td><td>prob:.50</td></tr><tr><th></th><td></td><td>D 0.20</td><td>Extinction:0</td><td></td></tr></tbody></table>
Data from: Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity
Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. Although methods for identifying evolutionary rate shifts in continuous characters have attracted recent attention (e.g. Eastman et al., 2011, Stack et al., 2011), such methods for discrete characters have only very recently been developed (Beaulieu et al., 2013, Beaulieu and O'Meara 2014) and have yet to be widely used. However, ancestral state reconstructions of discrete characters are being performed on increasingly large phylogenies, where it is likely that evolutionary rates will vary greatly between different clades (Beaulieu and O'Meara 2014). Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree, split BiSSE estimates separate rate parameters for pre-specified clades, and the hidden rates model partitions each character state into a number of rate categories. The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles. Additionally, simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades).
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