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Data for: Cephalopod Sex Determination and its Ancient Evolutionary Origin
<p>This repository contains the chromosome-level genome assembly, annotation, and genome hub files of the California two-spot octopus (<em>Octopus bimaculoides</em>). These data resulted in the discovery of the cephalopod sex chromosomes. Read the paper in <em>Current Biology </em>here: https://doi.org/10.1016/j.cub.2025.01.005. </p>
Data from: Evolutionary origins and diversification of proteobacterial mutualists
Mutualistic bacteria infect most eukaryotic species in nearly every biome. Nonetheless, two dilemmas remain unresolved about bacterial–eukaryote mutualisms: how do mutualist phenotypes originate in bacterial lineages and to what degree do mutualists traits drive or hinder bacterial diversification? Here, we reconstructed the phylogeny of the hyperdiverse phylum Proteobacteria to investigate the origins and evolutionary diversification of mutualistic bacterial phenotypes. Our ancestral state reconstructions (ASRs) inferred a range of 34–39 independent origins of mutualist phenotypes in Proteobacteria, revealing the surprising frequency with which host-beneficial traits have evolved in this phylum. We found proteobacterial mutualists to be more often derived from parasitic than from free-living ancestors, consistent with the untested paradigm that bacterial mutualists most often evolve from pathogens. Strikingly, we inferred that mutualists exhibit a negative net diversification rate (speciation minus extinction), which suggests that mutualism evolves primarily via transitions from other states rather than diversification within mutualist taxa. Moreover, our ASRs infer that proteobacterial mutualist lineages exhibit a paucity of reversals to parasitism or to free-living status. This evolutionary conservatism of mutualism is contrary to long-standing theory, which predicts that selection should often favour mutants in microbial mutualist populations that exploit or abandon more slowly evolving eukaryotic hosts.
FIG. 1 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 1.—Map of the Hawaiian Islands with collection sitesfor Hawaiian hoary bat tissues used inthis study. Sites with n> 1 are denoted with an asterisk.
FIG. 2 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 2.—PCA result plot showing clustering of individual bats from four Hawaiian Islands using 21,808,031 SNPs. Sample information included in supplementary table S4, Supplementary Material online.
FIG. 4 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations
FIG. 4.—SNAPP-based phylogenetic tree inference. (A) The maximum clade credibility or consensus tree, showing approximate divergence of hoary bats across the Hawaiian archipelago. The axis on the bottom of the figure corresponds to million years before present (Ma), using the emergence of Hawai'i (~0.43 Ma) as a calibration point (95% confidence intervals were given in square brackets). (B) The drawing of all sampled trees showing all ingroup nodes were supported by maximum posterior probabilities (1.00).
Figure 2 in Middle Miocene origins for tough-browse dietary specialisations in the koala (Marsupialia, Phascolarctidae) evolutionary tree: description of a new genus and species from the Riversleigh World Heritage Area
Figure 2. Stelakoala riversleighensis gen. et sp. nov. holotype (QM F57737) from Jim's Jaw Site, Riversleigh World Heritage Area, Qld. A-A', Occlusal stereopair; B, labelled occlusal view; C, lingual view; D, buccal view. Abbreviations: co, cristid obliqua; end, entoconid; esd, entostylid; er, entostylid ridge; hyd, hypoconid; lr, lingual ribs; med, metaconid; msd, metastylid; pad, paraconid; ppsd, preprotostylid cristid; prd, protoconid; psd, protostylid.
Figure 1 in Middle Miocene origins for tough-browse dietary specialisations in the koala (Marsupialia, Phascolarctidae) evolutionary tree: description of a new genus and species from the Riversleigh World Heritage Area
Figure 1. Map and regional schematic of the Riversleigh World Heritage Area (After Arena, 2005, and Megirian, 1992). The Type locality of Stelakoala riversleighensis gen. et sp. nov., Jim's Jaw Site, is located on the northern Gag Plateau (highlighted red).
Figure 3 in Middle Miocene origins for tough-browse dietary specialisations in the koala (Marsupialia, Phascolarctidae) evolutionary tree: description of a new genus and species from the Riversleigh World Heritage Area
Figure 3. The evolution of primary M1 trigonid cuspids (metaconid, protoconid and protostylid) in phascolarctids. A, Schematic diagram of a phascolarctid right M 1 illustrating how dimensions and percentages represented in Table 1 were obtained (adapted from Black et al., 2014a); B, Graphical representation of the relative positions and distance between the primary M 1 trigonid cuspids as a percentage of trigonid width; C, phylogenetic relationships of phascolarctids (from Black et al., 2012a). Abbreviations: end, entoconid; hyd, hypoconid; med, metaconid, prd, protoconid; psd, protostylid. Data for Madakoala, Perikoala, Litokoala, Nimiokoala and Phascolarctos, is based on M. devisi, Pe. robustus, L. kutjamarpensis, N. greystanesi and P. cinereus, respectively, with mean values used for the latter two species (Table 1).
FIGURE 10 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 10. Evolutionary and paleobiogeographic hypotheses proposed in this work illustrated with the plot of the first principal component for the lower dentition. Double horizontal lines indicate bidirectional migratory flows. Empty rectangles indicate the absence of barriers to dispersal between the last three regions considered, and solid rectangles indicate geographic isolation. See the text for a more detailed explanation.
FIGURE 9 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 9. Illustration of the two criteria used in this study as a practical guide to separate segments within a lineage. Successive values of a lineage with four populations and four fossils per population are shown. At the top, the range of variation observed for the variable considered in a related present-day biospecies. Taking the lowest value of the first population as an arbitrary reference point, the lineage will be divided into two segments for that time value at which the observed range for the biospecies is surpassed, and at the same time, the difference between the means of the two sets (C and C', respectively) becomes significant.
FIGURE 8 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 8. Relative size of the bone-breaking region of P4 versus the size of P4 for some localities of P. brevirostris. The correlation coefficient between both variables is significant (r = 0.844, p = 0.002). The ellipse corresponds to the expected region for the population at 95% confidence. Gi: Gigantopithecus Cave, Ke: Kedung Brubus, Lo: Longdan, LC: Longgu Cave, Re: Renzi Cave, Sa: Sainzelles, Um: Untermasfeld, Va: Val d'Arno, VM: Venta Micena, Yu: Yuanmou, Zo: Loc.1 of Zhoukoudian.
FIGURE 7 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 7. In A is shown a lateral view of an articulated skull and jaw of a H. hyaena specimen (EBD 33079M, Doñana Biological Station, Seville) and its corresponding schematic drawing in B, showing different functional regions of the dentition during the mandibular occlusion process. The main regions involved in cutting meat are the trigonid (Trig) of m1 in the lower dentition and the metastyle (Me) and the distal part of Paracone (P) of the upper fourth premolar (P4). The main elements involved in bone breaking are the two lower premolars (p4 and p3) that occlude with the upper third premolar (P3) and the mesial part of the paracone and the parastyle of the upper P4.
FIGURE 5 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 5. Bivariate plots of geological age on the scores for the lower dentition two first principal components. A-B, PC I for fossil individuals and paleontological localities, respectively. C-D, PC II for fossil individuals and paleontological localities, respectively. E: Elandsfontein. At the base of each figure are shown the ranges for the extant species and C. spelaea in each principal component.
FIGURE 4 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 4. Bivariate plots of the scores on the upper dentition two first principal components and their corresponding component loading plots for (A) analysis for fossil individuals and (B) analysis for paleontological localities. E: Elandsfontein. G: Gladysvale Cave. K: Kromdraai A. L: Longdan. S: Ségriès-le Réservoir.
FIGURE 2 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 2. Several examples of worn lower first molars. A, V 7296 from Baihaicum (from Qiu, 1987). B, Pliocrocuta perrieri (Se 312, Senèze, France). C, Crocuta crocuta (no id. Naturkundemuseum Berlin). D, plot of m1 trigonid length on m1 width for the species analyzed in this study. Note that there is a clear separation between Crocuta and Non Crocuta species. Additional explanations have been provided in the text.
FIGURE 1 in Unravelling the origin of the brown hyena (Parahyena brunnea) and its evolutionary and paleoecological implications for the Pachycrocuta lineage
FIGURE 1. Stratigraphic range of the species belonging to the analyzed lineages, their paleogeographic distribution (squares with gray background), and some examples of lower mandibles in labial view. IVPP V20801: Pliocrocuta perrieri from Zanclean (Zanda Basin, China), drawn from Tseng et al. (2016). KK 82-58: Parahyaena howelli (Laetoli, Tanzania), drawn from Werdelin and Dehghani (2011). MNHN 834: Pliocrocuta perrieri post-Zanclean (holotype from Mont Perrier, Muséum national d'histoire naturelle, Paris. C/C. 806: Pachycrocuta brevirostris (Zhoukoudian, China) drawn from Pei (1934). KA 55: Pachycrocuta bellax (Kromdraai A, South Africa) drawn from Ewer (1954a). 'Hyaena' prisca (holotype from Lunel-Viel, France) drawn from Brugal et al. (2021). NHM 35.9.1.286: Parahyaena brunnea (Karroo Valley, South Africa, housed at the Natural History Museum, London).
Fig. 9 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 9 Macroscopic symptoms of the infection of Juncus oxycarpus (a, healthy plant) roots by Juncorrhiza oxycarpi (b). Scale bars: a approx. 1 cm, b = 1 mm
Fig. 5 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 5 Macroscopic symptoms of the infection of Fuirena ciliaris roots by Entorrhiza fuirenae (arrows). Scale bar = approx. 1 cm
Fig. 7 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 7 Macroscopic symptoms of the infection of Juncus ranarius roots by Juncorrhiza maritima (arrows). Scale bar = 5 mm
Fig. 4 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 4 Tanglegram between host plant (left) and fungal (right) phylogenies reconstructed from the ITS + rbcL and ITS + LSU sequences, respectively. Nodal support is given as maximum likelihood bootstrap (≥
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