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180 results for “homoplasy”
Figure 13 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 13. Genitalia of Geminitor wenlockensis, QM MO86000 (holotype), Wenlock River. a) Reproductive system. b) Penis interior. Arrows mark the boundaries of the upper penial chamber. Scale bars: 1 mm.
Figure 10 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 10. Genitalia of Geminitor villaris. a). QM MO20887, Mt Cook. Reproductive system. b). AM C.553564, Mt Cook. Penis interior. c). QM MO20887, Mt Cook. Spermatophore. d-f). QM MO21256, Starcke. d). Reproductive system. e). Spermatophore. f). Penis interior. Scale bars: 1 mm.
Figure 11 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 11. Genitalia of Geminitor kullaensis, QM MO61687, Coen. a) Reproductive system. b) Penis interior. Arrows mark the boundaries of the upper penial chamber. Scale bars: 1 mm.
Figure 9 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 9. Genitalia of Geminitor laura, AM C.553551, Black Mountain. a). Reproductive system. b). Penis interior. Scale bars: 1 mm.
Figure 12 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 12. Genitalia of Geminitor macveae. a, b) QM MO85999 (holotype), Rifle Creek. a) Reproductive system. b) Penis interior. Scale bars: 1 mm.
Figure 8. Live animal images. a in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 8. Live animal images. a). Geminitor laura, Black Mountain. b). Geminitor villaris. c). Pravonitor aquilonia, AM C.524931, Bellenden Ker. d). Pravonitor aquilonia, Cape Tribulation. e). Pravonitor aquilonia, AM C.524981, Mossman Gorge. f). Elatonitor suturalis, Wooroonooran NP. Images not to scale. Photographs by Adnan Moussalli (a, d, f), Frank Köhler (c, e) and Queensland Museum (b).
Figure 7. Shell microsculpture. a–c in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 7. Shell microsculpture. a–c). Geminitor laura, AM C.553551, Black Mountain. d–f). Pravonitor aquilonia, AM C.553561, SE of Malanda. g–i). Elatonitor suturalis, QM MO76507, NE of Babinda. Scale bars: b, e, h = 200 µm; a, c, d, f, g, i = 500 µm. Photographs by Sue Lindsay.
Figure 6 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 6. Shells of Geminitor. a) Geminitor laura, AM C.474954, Lakeland Downs. b) Geminitor villaris, QM MO20887, Mt Cook. c) Geminitor villaris, QM MO21256, Starcke. d) Geminitor kullaensis, QM MO30875, McIlwraith Range. e) Geminitor macveae, QM MO20694 (paratype). f) Geminitor wenlockensis, QM MO86000 (H), Wenlock River. Scale bar: 5 mm. Photographs by F. Köhler ((a-b), d, f), J. Caiza (c), and G. Thompson (e).
Figure 4 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 4. Distribution map. Grey symbols: Geminitor. Blue symbols: Pravonitor. Red symbols: Elatonitor. Biogeographic barriers are marked in black; A = Normanby Basin, B = Black Mountain Corridor, and C = Atherton Tableland.
Figure 2 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 2. Majority-rule consensus tree based on Bayesian analysis of the concatenated data set of fragments of the mitochondrial genes 16S and COI. Ambiguous alignment sites in 16S removed using MAFFT. Numbers on branches indicate posterior probabilities. Scale bar indicates 7% of modelled sequence divergence. Individual samples are named as per their initial identification; genus and species names for a clade are based on the final taxonomic decisions.
Figure 21 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 21. Genitalia of Pravonitor stuarti, QM MO86002 (holotype), High Range. a) Reproductive system. b) Penis with tunica opened. c) Penis with tunica opened, opposite orientation to b). d) Penis interior. Scale bars: 1 mm.
Figure 1 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 1. Best maximum likelihood tree based on an analysis of the concatenated data set of fragments of the mitochondrial genes 16S and COI using IQ-TREE. Ambiguous alignment sites in 16S removed using MAFFT. Numbers on branches indicate nodal support based on 10,000 ultra-fast bootstrap repeats as well as by employing Shimodaira and Hasegawa's (1999)) approximate Likelihood Ratio Test ('SH-aLRT'). Scale bar indicates 7% of modelled sequence divergence. Individual samples are named as per their initial identification; genus and species names for a clade are based on the final taxonomic decisions.
Figure 15 in Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae)
Figure 15. Genitalia of Pravonitor annulus, QM MO15645, Yam Island. a) Reproductive system. b) penis interior. c) Spermatophore. Scale bars: 1 mm.
Data from: HExT, a software supporting tree-based screens for hybrid taxa in multilocus datasets, and an evaluation of the homoplasy excess test
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Data from: Examination of hemiplasy, homoplasy and phylogenetic discordance in chromosomal evolution of the Bovidae
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Data from: When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensis and M. paradoxus)
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Data from: Weighing homoplasy against alternative scenarios with the help of macroevolutionary modeling: a case study on limb bones of fossorial sciuromorph rodents
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Data from: When homoplasy is not homoplasy: dissecting trait evolution by contrasting composite and reductive coding
The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs reductive). Up to now, there is no common agreement to either code characters as complex or simple. Phylogeneticists have discussed which coding method is best, but have not incorporated the heuristic process of reciprocal illumination to evaluate the coding. Composite coding allows to test 1) if several characters were linked resulting in a structure described as a complex character or trait, or 2) if independently evolving characters resulted in the configuration incorrectly interpreted as a complex character. We propose that complex characters or character states should be decomposed iteratively into simpler characters when the original homology hypothesis is not corroborated by a phylogenetic analysis, and the character or character state is retrieved as homoplastic. We tested this approach using the case of fruit types within subfamily Cinchonoideae (Rubiaceae). The iterative reductive coding of characters associated to drupes allowed us to unthread fruit evolution within Cinchonoideae. Our results show that drupes and berries are not homologous. As a consequence, a more precise ontology for the Cinchonoideae drupes is required.
Data from: Homoplasy-based partitioning outperforms alternatives in Bayesian analysis of discrete morphological data
Bayesian analysis of morphological data is becoming increasingly popular mainly (but not only) because it allows for time-calibrated phylogenetic inference using relaxed morphological clocks and tip dating whenever fossils are available. As with molecular data, recent studies have shown that modeling among character rate variaton (ACRV) in morphological matrices greatly improves phylogenetic inference. In a likelihood framework this may be accomplished, for instance, by employing a hidden Markov model (HMM) to assign characters to rate categories drawn from a (discretized) Γ distribution and/or by partitioning datasets according to rate heterogeneity and estimating per-partition branch lengths, conditioned on a single topology. While the first approach is available in many phylogenetic analysis software, there is still no clear consensus on how to partition data, except perhaps in the simplest cases (e.g. "by codon" partitioning of coding sequences). Additionally, there is a trade-off between improvement in likelihood scores and the number of free parameters in the analysis, which rises quickly with the number of partitions. This trade-off may be dealt with by employing statistics that penalize overfitting of complex models, such as Akaike or Bayesian information criteria (AIC and BIC), or the more recently introduced stepping-stone (SS) method for marginal likelihood approximation. We applied the latter to three distinct matrices of discrete morphological data and demonstrated that sorting characters by homoplasy scores (obtained from implied weighting parsimony analysis) outperformed other partitioning strategies (anatomically-based and PartitionFinder2). The method was in fact so efficient in segregating characters by rates of evolution that no within-partition ACRV modeling was necessary, while among partition rate variation (APRV) was adequately accommodated by rate multipliers. We conclude that partitioning by homoplasy is a powerful and easy-to-implement strategy to address ACRV in complex datasets. We provide some guidelines focusing on morphological matrices, although this approach may be also applicable to molecular datasets.
Data from: Evolution of the snake body form reveals homoplasy in amniote Hox gene function
Hox genes regulate regionalization of the axial skeleton in vertebrates, and changes in their expression have been proposed to be a fundamental mechanism driving the evolution of new body forms. The origin of the snake-like body form, with its deregionalized pre-cloacal axial skeleton, has been explained as either homogenization of Hox gene expression domains9, or retention of standard vertebrate Hox domains with alteration of downstream expression that suppresses development of distinct regions. Both models assume a highly regionalized ancestor, but the extent of deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the skeleton in snake-like body forms has never been analysed. Here we combine geometric morphometrics and maximum-likelihood analysis to show that the pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes is not deregionalized compared with limbed taxa, and that the phylogenetic structure of primaxial morphology in reptiles does not support a loss of regionalization in the evolution of snakes. We demonstrate that morphometric regional boundaries correspond to mapped gene expression domains in snakes, suggesting that their primaxial domain is patterned by a normally functional Hox code. Comparison of primaxial osteology in fossil and modern amniotes with Hox gene distributions within Amniota indicates that a functional, sequentially expressed Hox code patterned a subtle morphological gradient along the anterior–posterior axis in stem members of amniote clades and extant lizards, including snakes. The highly regionalized skeletons of extant archosaurs and mammals result from independent evolution in the Hox code and do not represent ancestral conditions for clades with snake-like body forms. The developmental origin of snakes is best explained by decoupling of the primaxial and abaxial domains and by increases in somite number, not by changes in the function of primaxial Hox genes.
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