1
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Li YD, Tomaszewska W, Arriaga-Varela E, Huang DY, Cai CY. An unusual Cretaceous beetle with affinity to Anamorphidae (Coleoptera: Coccinelloidea). PeerJ 2024; 12:e18008. [PMID: 39301060 PMCID: PMC11412222 DOI: 10.7717/peerj.18008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/09/2024] [Indexed: 09/22/2024] Open
Abstract
Coccinelloid beetles have a sparse fossil record in the Mesozoic. Here, we describe and illustrate an unusual coccinelloid beetle, Yassibum yoshitomii gen. et sp. nov., from mid-Cretaceous Kachin amber. Yassibum stands out within the Coccinelloidea due to its notched profemora and the presence of antennal grooves on the elytral epipleura. Based on our phylogenetic analyses, we suggest that Yassibum is most likely related to the family Anamorphidae. The alternative placements are critically evaluated based on our comparison of the morphology.
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Affiliation(s)
- Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | | | | | - Di-Ying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Chen-Yang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
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2
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Döcker J, Linz S, Wicke K. Bounding the Softwired Parsimony Score of a Phylogenetic Network. Bull Math Biol 2024; 86:121. [PMID: 39174812 PMCID: PMC11341636 DOI: 10.1007/s11538-024-01350-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024]
Abstract
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.
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Affiliation(s)
- Janosch Döcker
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Simone Linz
- School of Computer Science, University of Auckland, Auckland, New Zealand.
| | - Kristina Wicke
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, USA
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3
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Arriaga-Varela E, Szawaryn K, Zhou YL, Bruthansová J, Li YD, Tomaszewska W. Early evolution of Anamorphidae (Coleoptera: Coccinelloidea): the oldest known anamorphid beetles from Upper Cretaceous amber of northern Myanmar and the first report of potential glandular pores in the family. Cladistics 2024; 40:411-429. [PMID: 38573084 DOI: 10.1111/cla.12576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
In order to place newly discovered fossil taxa (Palaeosymbius gen. nov. with P. groehni and P. mesozoicus spp. nov.) from the mid-Cretaceous amber from northern Myanmar, we investigated the relations of extant and extinct lineages of the coccinellid group of Coccinelloidea with emphasis on the family Anamorphidae. We assembled a taxonomic sampling of 34 taxa, including 15 genera and 19 species of Anamorphidae, the most comprehensive sampling of Anamorphidae at the generic level in a phylogenetic analysis. A morphological dataset of 47 characters was built as well as a molecular alignment of 7140 bp including fragments of eight genes (12S, 16S, 18S, 28S, COI, COII, H3 and CAD). Five anamorphid and one endomychid species were sequenced for the first time and added to the dataset. We performed parsimony-based analysis of the morphological dataset and Bayesian inference analysis of the combined matrix (morphological plus molecular data). Our results confirm that Palaeosymbius belongs to Anamorphidae and represents the oldest known member of this family so far. Among Anamorphidae, Symbiotes (with extant and known Eocene species) was recovered as the most probable closest relative of Palaeosymbius. Our morphological studies additionally revealed the presence of probable glandular openings in the anterolateral corners of the pronotal margins in Asymbius sp. and Anamorphus sp., representing the first report of secretory openings in the family Anamorphidae. Similar openings are found in other cucujiform beetles such as Cryptophagidae and Boganiidae with possible defensive purposes.
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Affiliation(s)
- Emmanuel Arriaga-Varela
- Museum and Institute of Zoology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
- Red de Biodiversidad y Sistemática, Carretera Antigua a Coatepec, Instituto de Ecología, A.C., 351, El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Karol Szawaryn
- Museum and Institute of Zoology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
| | - Yu-Lingzi Zhou
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia
| | - Jana Bruthansová
- Department of Paleontology, National Museum, Prague, Czech Republic
| | - Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Wioletta Tomaszewska
- Museum and Institute of Zoology, Polish Academy of Sciences, Twarda 51/55, 00-818, Warsaw, Poland
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4
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Fleming J, Eriksen PM, Struck TH. Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric. F1000Res 2024; 12:945. [PMID: 38799242 PMCID: PMC11128044 DOI: 10.12688/f1000research.139356.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/05/2024] [Indexed: 05/29/2024] Open
Abstract
Background: The phylogenetic bootstrap, first proposed by Felsenstein in 1985, is a critically important statistical method in assessing the robusticity of phylogenetic datasets. Core to its concept was the use of pseudo sampling - assessing the data by generating new replicates derived from the initial dataset that was used to generate the phylogeny. In this way, phylogenetic support metrics could overcome the lack of perfect, infinite data. With infinite data, however, it is possible to sample smaller replicates directly from the data to obtain both the phylogeny and its statistical robusticity in the same analysis. Due to the growth of whole genome sequencing, the depth and breadth of our datasets have greatly expanded and are set to only expand further. With genome-scale datasets comprising thousands of genes, we can now obtain a proxy for infinite data. Accordingly, we can potentially abandon the notion of pseudo sampling and instead randomly sample small subsets of genes from the thousands of genes in our analyses. Methods: We introduce Scoutknife, a jackknife-style subsampling implementation that generates 100 datasets by randomly sampling a small number of genes from an initial large-gene dataset to jointly establish both a phylogenetic hypothesis and assess its robusticity. We assess its effectiveness by using 18 previously published datasets and 100 simulation studies. Results: We show that Scoutknife is conservative and informative as to conflicts and incongruence across the whole genome, without the need for subsampling based on traditional model selection criteria. Conclusions: Scoutknife reliably achieves comparable results to selecting the best genes on both real and simulation datasets, while being resistant to the potential biases caused by selecting for model fit. As the amount of genome data grows, it becomes an even more exciting option to assess the robusticity of phylogenetic hypotheses.
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Affiliation(s)
- James Fleming
- Natural History Museum, Universitetet i Oslo, Oslo, Oslo, 0562, Norway
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5
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Li Y, Kolibáč J, Liu Z, Ślipiński A, Yamamoto S, Yu Y, Zhang W, Cai C. Foveapeltis gen. nov., an unusual cleroid genus with large hypomeral cavities from mid-Cretaceous amber (Coleoptera: Cleroidea). Ecol Evol 2024; 14:e11589. [PMID: 38979007 PMCID: PMC11229430 DOI: 10.1002/ece3.11589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/22/2024] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Beetles have a remote evolutionary history dating back to the Carboniferous, with Mesozoic fossils playing a pivotal role in elucidating the early evolution of extant families. Despite their exceptional preservation in amber, deciphering the systematic positions of Mesozoic trogossitid-like beetles remains challenging. Here, we describe and illustrate a new trogossitid-like lineage from mid-Cretaceous Kachin amber, Foveapeltis rutai Li, Kolibáč, Liu & Cai, gen. et sp. nov. Foveapeltis stands out within the Cleroidea due to the presence of a significant large cavity on each hypomeron. While the exact phylogenetic placement of Foveapeltis remains uncertain, we offer a discussion on its potential affinity based on our constrained phylogenetic analyses.
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Affiliation(s)
- Yan‐Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjingChina
- Bristol Palaeobiology Group, School of Earth SciencesUniversity of BristolBristolUK
| | - Jiří Kolibáč
- Department of EntomologyMoravian MuseumBrnoCzech Republic
| | - Zhen‐Hua Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
| | - Adam Ślipiński
- Australian National Insect CollectionCSIROCanberraAustralian Capital TerritoryAustralia
| | | | - Ya‐Li Yu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of ZoologyGuangdong Academy of SciencesGuangzhouChina
| | - Wei‐Ting Zhang
- Institute of PaleontologyHebei GEO UniversityShijiazhuangChina
| | - Chen‐Yang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjingChina
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6
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Ezcurra MD. Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices. Cladistics 2024; 40:242-281. [PMID: 38728134 DOI: 10.1111/cla.12581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimony analyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogenetic matrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stability of results for alternative character weighting methods directly on empirical data. Each generation was compared against the most recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised (fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on six different genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k) between 3 and 30. Pairwise comparisons between trees were conducted using Robinson-Foulds distances normalized by the total number of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities. The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in the vast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originally analysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distances based on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the most similar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimal k-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values to be used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a low sample size of genealogies.
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Affiliation(s)
- Martín D Ezcurra
- Sección Paleontología de Vertebrados, CONICET-Museo Argentino de Ciencias Naturales, Ángel Gallardo 470, C1405DJR, Ciudad Autónoma de Buenos Aires, Argentina
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, Birmingham, UK
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7
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Rick JA, Brock CD, Lewanski AL, Golcher-Benavides J, Wagner CE. Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses. Syst Biol 2024; 73:76-101. [PMID: 37881861 DOI: 10.1093/sysbio/syad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023] Open
Abstract
Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.
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Affiliation(s)
- Jessica A Rick
- School of Natural Resources & the Environment, University of Arizona, Tucson, AZ 85719, USA
| | - Chad D Brock
- Department of Biological Sciences, Tarleton State University, Stephenville, TX 76401, USA
| | - Alexander L Lewanski
- Department of Integrative Biology and W.K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Jimena Golcher-Benavides
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA 50011, USA
| | - Catherine E Wagner
- Program in Ecology and Evolution, University of Wyoming, Laramie, WY 82071, USA
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA
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8
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Li YD, Liu ZH, Huang DY, Cai CY. An enigmatic Cretaceous beetle with possible affinity to Erotylidae (Coleoptera: Cucujiformia). CURRENT RESEARCH IN INSECT SCIENCE 2024; 5:100075. [PMID: 38374887 PMCID: PMC10875113 DOI: 10.1016/j.cris.2024.100075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
The morphology of beetles of the recently defined superfamilies Erotyloidea, Nitiduloidea and Cucujoidea is varied. Determining the systematic positions of Mesozoic fossils within these groups can often be challenging. Here we describe and illustrate a puzzling cucujiform beetle, Isocryptophilus exilipunctus Li & Cai gen. & sp. nov., based on an individual from mid-Cretaceous Burmese amber. While we cannot definitively pinpoint the exact phylogenetic position of Isocryptophilus, its possible affinity to Erotylidae is discussed in light of our phylogenetic analyses. A broader-sampled morphological matrix, coupled with a robust molecular phylogeny of these groups, will be promising for clarifying the systematic placement of the fossil.
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Affiliation(s)
- Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Zhen-Hua Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Di-Ying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chen-Yang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
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9
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Coiro M. Embracing uncertainty: The way forward in plant fossil phylogenetics. AMERICAN JOURNAL OF BOTANY 2024; 111:e16282. [PMID: 38334302 DOI: 10.1002/ajb2.16282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 02/10/2024]
Abstract
Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution. This low support is due to the pervasiveness of morphological convergence among plant organs and the fragmentary nature of many plant fossils, and it is often perceived as a fundamental weakness reducing the utility of plant fossils in phylogenetics. Here I discuss the importance of uncertainty in morphological phylogenetics and how we can identify important information from different patterns and types of uncertainty. I also review a set of methodologies that can allow us to understand the causes underpinning uncertainty and how these practices can help us to further our knowledge of plant fossils. I also propose that a new visual language, including the use of networks instead of trees, represents an improvement on the old visualization based on consensus trees and more adequately serves phylogeneticists working with plant fossils. This set of methods and visualization tools represents an important way forward in a fundamental field for our understanding of the evolutionary history of plants.
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Affiliation(s)
- Mario Coiro
- Department of Palaeontology, University of Vienna, Vienna, Austria
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA
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10
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Francisco Barbosa F, Mermudes JRM, Russo CAM. Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny. PeerJ 2024; 12:e16706. [PMID: 38213769 PMCID: PMC10782957 DOI: 10.7717/peerj.16706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson-Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless' consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal.
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Affiliation(s)
| | | | - Claudia A. M. Russo
- Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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11
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Simmons MP, Goloboff PA, Stöver BC, Springer MS, Gatesy J. Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses. Cladistics 2023; 39:418-436. [PMID: 37096985 DOI: 10.1111/cla.12540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/22/2023] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-tree branches with 0% approximate-likelihood-ratio-test (SH-like aLRT) support in likelihood analyses and strict consensus trees for parsimony, and then subsampled those partially resolved trees based on congruence measures that do not penalize polytomies. For this purpose we developed a new TNT script for congruence sorting (congsort), and used it to calculate topological incongruence for eight phylogenomic datasets using three distance measures: standard Robinson-Foulds (RF) distances; overall success of resolution (OSR), which is based on counting both matching and contradicting clades; and RF contradictions, which only counts contradictory clades. As expected, we found that gene-tree incongruence was often concentrated in clades that are arbitrarily or dubiously resolved and that there was greater congruence between the partially collapsed gene trees and the coalescent and concatenation topologies inferred from those genes. Coalescent branch lengths typically increased as the most incongruent gene trees were excluded, although branch supports typically did not. We investigated two successful and complementary approaches to prioritizing genes for investigation of alignment or homology errors. Coalescent-tree clades that contradicted concatenation-tree clades were generally less robust to gene-tree subsampling than congruent clades. Our preferred approach to collapsing likelihood gene-tree clades (0% SH-like aLRT support) and subsampling those trees (OSR) generally outperformed competing approaches for a large fungal dataset with respect to branch lengths, support and congruence. We recommend widespread application of this approach (and strict consensus trees for parsimony-based analyses) for improving quantification of gene-tree congruence/conflict, estimating coalescent branch lengths, testing robustness of coalescent analyses to gene-tree-estimation error, and improving topological robustness of summary coalescent analyses. This approach is quick and easy to implement, even for huge datasets.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Pablo A Goloboff
- CONICET, INSUE, Fundación Miguel Lillo, Miguel Lillo 251, 4000, S.M. de Tucumán, Argentina
| | - Ben C Stöver
- Institute for Evolution and Biodiversity, WMU Münster, 48149, Münster, Germany
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
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12
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Prusokiene A, Prusokas A, Retkute R. Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes. NAR Genom Bioinform 2023; 5:lqad077. [PMID: 37608801 PMCID: PMC10440785 DOI: 10.1093/nargab/lqad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/26/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
Tracking cells as they divide and progress through differentiation is a fundamental step in understanding many biological processes, such as the development of organisms and progression of diseases. In this study, we investigate a machine learning approach to reconstruct lineage trees in experimental systems based on mutating synthetic genomic barcodes. We refine previously proposed methodology by embedding information of higher level relationships between cells and single-cell barcode values into a feature space. We test performance of the algorithm on shallow trees (up to 100 cells) and deep trees (up to 10 000 cells). Our proposed algorithm can improve tree reconstruction accuracy in comparison to reconstructions based on a maximum parsimony method, but this comes at a higher computational time requirement.
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Affiliation(s)
- Alisa Prusokiene
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Renata Retkute
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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13
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Laboury A, Scheyer TM, Klein N, Stubbs TL, Fischer V. High phenotypic plasticity at the dawn of the eosauropterygian radiation. PeerJ 2023; 11:e15776. [PMID: 37671356 PMCID: PMC10476616 DOI: 10.7717/peerj.15776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/29/2023] [Indexed: 09/07/2023] Open
Abstract
The initial radiation of Eosauropterygia during the Triassic biotic recovery represents a key event in the dominance of reptiles secondarily adapted to marine environments. Recent studies on Mesozoic marine reptile disparity highlighted that eosauropterygians had their greatest morphological diversity during the Middle Triassic, with the co-occurrence of Pachypleurosauroidea, Nothosauroidea and Pistosauroidea, mostly along the margins of the Tethys Ocean. However, these previous studies quantitatively analysed the disparity of Eosauropterygia as a whole without focussing on Triassic taxa, thus limiting our understanding of their diversification and morphospace occupation during the Middle Triassic. Our multivariate morphometric analyses highlight a clearly distinct colonization of the ecomorphospace by the three clades, with no evidence of whole-body convergent evolution with the exception of the peculiar pistosauroid Wangosaurus brevirostris, which appears phenotypically much more similar to nothosauroids. This global pattern is mostly driven by craniodental differences and inferred feeding specializations. We also reveal noticeable regional differences among nothosauroids and pachypleurosauroids of which the latter likely experienced a remarkable diversification in the eastern Tethys during the Pelsonian. Our results demonstrate that the high phenotypic plasticity characterizing the evolution of the pelagic plesiosaurians was already present in their Triassic ancestors, casting eosauropterygians as particularly adaptable animals.
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Affiliation(s)
- Antoine Laboury
- Evolution & Diversity Dynamics Lab, Université de Liège, Liège, Belgium
| | | | - Nicole Klein
- Institute of Geosciences, Paleontology, University of Bonn, Bonn, Germany
| | - Thomas L. Stubbs
- School of Life, Health & Chemical Sciences, Open University, Milton Keynes, United Kingdom
| | - Valentin Fischer
- Evolution & Diversity Dynamics Lab, Université de Liège, Liège, Belgium
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14
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Keating JN, Garwood RJ, Sansom RS. Phylogenetic congruence, conflict and consilience between molecular and morphological data. BMC Ecol Evol 2023; 23:30. [PMID: 37403037 DOI: 10.1186/s12862-023-02131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/08/2023] [Indexed: 07/06/2023] Open
Abstract
Morphology and molecules are important data sources for estimating evolutionary relationships. Modern studies often utilise morphological and molecular partitions alongside each other in combined analyses. However, the effect of combining phenomic and genomic partitions is unclear. This is exacerbated by their size imbalance, and conflict over the efficacy of different inference methods when using morphological characters. To systematically address the effect of topological incongruence, size imbalance, and tree inference methods, we conduct a meta-analysis of 32 combined (molecular + morphology) datasets across metazoa. Our results reveal that morphological-molecular topological incongruence is pervasive: these data partitions yield very different trees, irrespective of which method is used for morphology inference. Analysis of the combined data often yields unique trees that are not sampled by either partition individually, even with the inclusion of relatively small quantities of morphological characters. Differences between morphology inference methods in terms of resolution and congruence largely relate to consensus methods. Furthermore, stepping stone Bayes factor analyses reveal that morphological and molecular partitions are not consistently combinable, i.e. data partitions are not always best explained under a single evolutionary process. In light of these results, we advise that the congruence between morphological and molecular data partitions needs to be considered in combined analyses. Nonetheless, our results reveal that, for most datasets, morphology and molecules can, and should, be combined in order to best estimate evolutionary history and reveal hidden support for novel relationships. Studies that analyse only phenomic or genomic data in isolation are unlikely to provide the full evolutionary picture.
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Affiliation(s)
- Joseph N Keating
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Russell J Garwood
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
- Natural History Museum, London, SW7 5BD, UK
| | - Robert S Sansom
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK.
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15
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Simões TR, Vernygora OV, de Medeiros BAS, Wright AM. Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data. Syst Biol 2023; 72:662-680. [PMID: 36773019 PMCID: PMC10276625 DOI: 10.1093/sysbio/syad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/08/2022] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].
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Affiliation(s)
- Tiago R Simões
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Oksana V Vernygora
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | | | - April M Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, USA
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16
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Kolibáč J. A new species of the rare monotypic genus Cyrtinoclerus Chapin from Borneo, with notes on Meprinogenus Kolibáč (Coleoptera: Thanerocleridae). Zootaxa 2023; 5271:569-578. [PMID: 37518109 DOI: 10.11646/zootaxa.5271.3.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 08/01/2023]
Abstract
Cyrtinoclerus sabahensis sp. nov. of the less diverse cleroid family Thanerocleridae is described from Borneo. The unique specimen was found in the Malaysian state of Sabah and represents the first collecting record of the genus in one hundred years. The new species is assigned to the hitherto monotypic genus Cyrtinoclerus Chapin, 1924, whose single species is known from a single specimen from Basilan, Philippines, with no subsequently collected specimens known to date. Cyrtinoclerus is distinct in its unique synapomorphies, namely the tarsi with formula 5-5-5 but tarsomeres 4 reduced in size, elytron depressed in basal third with distinct bulge, and seriate punctation of elytra. The genus is re-examined and again classified within Thanerocleridae. A systematic status of Cyrtinoclerus and its relative Meprinogenus Kolibáč, 1992, also known only from two just one-hundred-year-old specimens, is discussed and possible synonymy of the latter genus suggested. The family Thanerocleridae now comprises 38 extant species in eleven genera and four extinct Cretaceous genera and species found in Burmese and Charentese ambers. A phylogenetic analysis of all fifteen extinct and extant genera of Thanerocleridae based on 36 morphological characters is presented and updated key to the tribe Thaneroclerini provided.
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Affiliation(s)
- Jiří Kolibáč
- Moravian Museum; Department of Entomology; Hviezdoslavova 29a; 62700 Brno; Czechia.
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17
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Morales ME, Goloboff PA. New TNT routines for parallel computing with MPI. Mol Phylogenet Evol 2023; 178:107643. [PMID: 36216302 DOI: 10.1016/j.ympev.2022.107643] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022]
Abstract
Phylogenetic inference, which involves time-consuming calculations, is a field where parallelization can speed up the resolution of many problems. TNT (a widely used program for phylogenetic analysis under parsimony) allows parallelization under the PVM system (Parallel Virtual Machine). However, as the basic aspects of the implementation remain unpublished, few studies have taken advantage of the parallelization routines of TNT. In addition, the PVM system is deprecated by many system administrators. One of the most common standards for high performance computing is now MPI (Message Passing Interface). To facilitate the use of the parallel analyses offered by TNT, this paper describes the basic aspects of the implementation, as well as a port of the parallelization interface of TNT into MPI. The use of the new routines is illustrated by reanalysis of seven significant datasets, either recent phylogenomic datasets with many characters (up to 2,509,064 characters) or datasets with large numbers of taxa (up to 13,921 taxa). Versions of TNT including the MPI functionality are available at: http://www.lillo.org.ar/phylogeny/tnt/.
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Affiliation(s)
- Martín E Morales
- Unidad Ejecutora Lillo (Fundación Miguel Lillo - Consejo Nacional de Investigaciones Científicas y Técnicas), Miguel Lillo 251, S. M. de Tucumán 4000, Argentina
| | - Pablo A Goloboff
- Unidad Ejecutora Lillo (Fundación Miguel Lillo - Consejo Nacional de Investigaciones Científicas y Técnicas), Miguel Lillo 251, S. M. de Tucumán 4000, Argentina; American Museum of Natural History, Central Park West at 79th Street, New York, United States.
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18
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Li YD, Yamamoto S, Newton AF, Cai CY. Kekveus brevisulcatus sp. nov., a new featherwing beetle from mid-Cretaceous amber of northern Myanmar (Coleoptera: Ptiliidae). PeerJ 2023; 11:e15306. [PMID: 37193020 PMCID: PMC10183168 DOI: 10.7717/peerj.15306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/06/2023] [Indexed: 05/18/2023] Open
Abstract
Ptiliidae (featherwing beetles) is a group of minute staphylinoid beetles with a scarce fossil record. Here a second member of the Mesozoic genus Kekveus Yamamoto et al. is reported from mid-Cretaceous Burmese amber, with detailed morphology obtained through confocal microscopy. Kekveus brevisulcatus Li, Yamamoto, Newton & Cai sp. nov. shares with K. jason Yamamoto et al. the unpaired medial pronotal fovea and narrowly separated transverse metacoxae, but can be separated from the latter based on its less elongate body, shorter pronotal foveae, and much weaker transverse depression on the head. Our phylogenetic analyses support the discheramocephalin affinity of Kekveus, although its relationship with other members of Discheramocephalini cannot be confidently resolved.
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Affiliation(s)
- Yan-Da Li
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Shûhei Yamamoto
- The Hokkaido University Museum, Hokkaido University, Sapporo, Japan
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States of America
| | - Alfred F. Newton
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States of America
| | - Chen-Yang Cai
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
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19
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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20
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Li YD, Leschen RAB, Liu ZH, Huang DY, Cai CY. An enigmatic beetle with affinity to Lamingtoniidae in mid-Cretaceous amber from northern Myanmar (Coleoptera: Cucujoidea). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.972343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
An enigmatic cucujiform beetle, Alloterocucus atratus Li, Leschen, Liu, and Cai gen. et sp. nov., is reported from mid-Cretaceous Burmese amber. The character combination of the new fossil is not completely consistent with any of the known cucujoid or erotyloid families. Based on our phylogenetic analyses, Alloterocucus is assigned to Cucujoidea and may be allied to Lamingtoniidae, which contains a single Australasian genus in the extant fauna. Alloterocucus shares with Lamingtoniidae a similar habitus and a series of characters, including the absence of postocular constriction, 3-segmented antennal club, externally open procoxal cavities, laterally open mesocoxal cavities, exposed pro- and mesotrochantins, and the absence of epipleural fovea and pronotal setose cavities, but differs from extant Lamingtoniidae in its apically truncate terminal maxillary palpomeres, 5-5-4 tarsi in male and absence of distinct dorsal punctation.Zoobank registration[https://zoobank.org/], identifier [111CE15E-5B49-4154-9E4A-7B3A738C6D2A].
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21
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Li YD, Ruta R, Tihelka E, Liu ZH, Huang DY, Cai CY. A new marsh beetle from mid-Cretaceous amber of northern Myanmar (Coleoptera: Scirtidae). Sci Rep 2022; 12:13403. [PMID: 35927559 PMCID: PMC9352693 DOI: 10.1038/s41598-022-16822-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
As one of the earliest-diverging lineage of the megadiverse beetle suborder Polyphaga, marsh beetles (Scirtidae) are crucial for reconstructing the ancestor of all polyphagan beetles and the ecomorphological underpinnings of their remarkable evolutionary success. The phylogeny of marsh beetles has nonetheless remained challenging to infer, not least because of their fragmentary Mesozoic fossil record. Here we describe a new scirtid beetle genus and species, Varcalium lawrencei gen. et sp. nov., preserving internal tissue, from Albian–Cenomanian Kachin amber (ca 99 Ma), representing the second member of this family known from the deposit. Based on a formal morphological phylogenetic analysis, Varcalium is recovered within the crown-group of Scirtinae, forming a clade with other genera that possess subocular carinae. The finding suggests that the crown-group of Scirtinae has already diversified by the mid-Cretaceous.
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Affiliation(s)
- Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Rafał Ruta
- Department of Biodiversity and Evolutionary Taxonomy, University of Wrocław, Przybyszewskiego 65, 51-148, Wrocław, Poland
| | - Erik Tihelka
- School of Earth Sciences, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Zhen-Hua Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.,Australian National Insect Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Di-Ying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Chen-Yang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China. .,School of Earth Sciences, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK.
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22
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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23
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Li YD, Newton AF, Huang DY, Cai CY. The First Fossil of Nossidiinae From Mid-Cretaceous Amber of Northern Myanmar (Coleoptera: Ptiliidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.911512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ptiliidae is a group of distinctly miniaturized staphylinoid beetles with a scarce fossil record. Here, we report a new ptiliid genus and species, Crenossidium slipinskii Li, Newton and Cai gen. et sp. nov., from mid-Cretaceous amber from northern Myanmar. Crenossidium can be attributed to the subfamily Nossidiinae based on the hind wing morphology, which has also been confirmed through phylogenetic analyses. Crenossidium differs from other extant nossidiine genera in the combination of the wide apical maxillary palpomeres, posteriorly widest pronotal disk, (almost) contiguous procoxae, fewer setae along wing margin, and multidentate pygidium.urn:lsid:zoobank.org:pub:8038D763-6856-4AC5-972C-E20D636137EE.
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24
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Molecular phylogenies map to biogeography better than morphological ones. Commun Biol 2022; 5:521. [PMID: 35641555 PMCID: PMC9156683 DOI: 10.1038/s42003-022-03482-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable. Using biogeographical and phylogenetic data, it is shown that molecular trees fit species geographical data better than trees inferred from morphology, and that these differences are not simply due to better tree resolution.
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25
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Peris D, Mähler B, Kolibáč J. Review of the Family Thanerocleridae (Coleoptera: Cleroidea) and the Description of Thanerosus gen. nov. from Cretaceous Amber Using Micro-CT Scanning. INSECTS 2022; 13:insects13050438. [PMID: 35621774 PMCID: PMC9147608 DOI: 10.3390/insects13050438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/27/2023]
Abstract
The predaceous beetle family Thanerocleridae is one of the smallest families of Cleroidea. It comprises only 36 extant species widespread on all continents. Three more species have been described from Cretaceous ambers of Myanmar and France. The fourth fossil representative of Thanerocleridae is described herein. Thanerosus antiquus gen. and sp. nov. is based on one fossil specimen preserved in an amber piece from Upper Cretaceous Kachin amber. The holotype was imaged using an X-ray micro-CT system to obtain high-quality 3D images. A phylogenetic analysis based on 33 morphological characters supports the placement of the new genus at the basal position in a tree of Thanerocleridae, in the vicinity of extant Zenodosus Wolcott and three extinct Mesozoic genera with which the new fossil shares open procoxal and mesocoxal cavities and transverse procoxae. We offer here a key to all extant and extinct genera in the family together with a complete list of all valid thaneroclerid taxa.
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Affiliation(s)
- David Peris
- Departament de Dinàmica de la Terra i de l’Oceà, Facultat de Ciències de la Terra, Universitat de Barcelona, 08028 Barcelona, Spain;
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Bastian Mähler
- Institute of Geosciences, Section Paleontology, University of Bonn, 53115 Bonn, Germany;
| | - Jiří Kolibáč
- Department of Entomology, Moravian Museum, 62700 Brno, Czech Republic
- Correspondence:
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26
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Chani-Posse MR, Ramírez-Salamanca JM, Silva-Tavera DF. Chani-Posse et al.: A new rove-beetle Neotropical genus systematic treatment of the Neotropical Philonthina (Coleoptera, Staphylinidae, Staphylinini): Carmenlyrus gen. nov. and its phylogenetic relationships. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Pohle A, Kröger B, Warnock RCM, King AH, Evans DH, Aubrechtová M, Cichowolski M, Fang X, Klug C. Early cephalopod evolution clarified through Bayesian phylogenetic inference. BMC Biol 2022; 20:88. [PMID: 35421982 PMCID: PMC9008929 DOI: 10.1186/s12915-022-01284-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 03/22/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Despite the excellent fossil record of cephalopods, their early evolution is poorly understood. Different, partly incompatible phylogenetic hypotheses have been proposed in the past, which reflected individual author's opinions on the importance of certain characters but were not based on thorough cladistic analyses. At the same time, methods of phylogenetic inference have undergone substantial improvements. For fossil datasets, which typically only include morphological data, Bayesian inference and in particular the introduction of the fossilized birth-death model have opened new possibilities. Nevertheless, many tree topologies recovered from these new methods reflect large uncertainties, which have led to discussions on how to best summarize the information contained in the posterior set of trees. RESULTS We present a large, newly compiled morphological character matrix of Cambrian and Ordovician cephalopods to conduct a comprehensive phylogenetic analysis and resolve existing controversies. Our results recover three major monophyletic groups, which correspond to the previously recognized Endoceratoidea, Multiceratoidea, and Orthoceratoidea, though comprising slightly different taxa. In addition, many Cambrian and Early Ordovician representatives of the Ellesmerocerida and Plectronocerida were recovered near the root. The Ellesmerocerida is para- and polyphyletic, with some of its members recovered among the Multiceratoidea and early Endoceratoidea. These relationships are robust against modifications of the dataset. While our trees initially seem to reflect large uncertainties, these are mainly a consequence of the way clade support is measured. We show that clade posterior probabilities and tree similarity metrics often underestimate congruence between trees, especially if wildcard taxa are involved. CONCLUSIONS Our results provide important insights into the earliest evolution of cephalopods and clarify evolutionary pathways. We provide a classification scheme that is based on a robust phylogenetic analysis. Moreover, we provide some general insights on the application of Bayesian phylogenetic inference on morphological datasets. We support earlier findings that quartet similarity metrics should be preferred over the Robinson-Foulds distance when higher-level phylogenetic relationships are of interest and propose that using a posteriori pruned maximum clade credibility trees help in assessing support for phylogenetic relationships among a set of relevant taxa, because they provide clade support values that better reflect the phylogenetic signal.
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Affiliation(s)
- Alexander Pohle
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, CH-8006, Zürich, Switzerland.
| | - Björn Kröger
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 44, Jyrängöntie 2, FI-00014, Helsinki, Finland
| | - Rachel C M Warnock
- GeoZentrum Nordbayern, Friedrich-Alexander Universität Erlangen-Nürnberg, Loewenichstrasse 28, 91054, Erlangen, Germany
| | - Andy H King
- Geckoella Ltd, Suite 323, 7 Bridge Street, Taunton, TA1 1TG, UK
| | - David H Evans
- Natural England, Rivers House, East Quay, Bridgwater, TA6 4YS, UK
| | - Martina Aubrechtová
- Institute of Geology and Palaeontology, Faculty of Science, Charles University, Albertov 6, 12843, Prague, Czech Republic
- Institute of Geology, Czech Academy of Sciences, Rozvojová 269, 16500, Prague, Czech Republic
| | - Marcela Cichowolski
- Instituto de Estudios Andinos "Don Pablo Groeber", CONICET and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, C1428EGA, Buenos Aires, Argentina
| | - Xiang Fang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 39 East Beijing Road, Nanjing, 210008, China
| | - Christian Klug
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, CH-8006, Zürich, Switzerland
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Tumescheit C, Firth AE, Brown K. CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments. PeerJ 2022; 10:e12983. [PMID: 35310163 PMCID: PMC8932311 DOI: 10.7717/peerj.12983] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/01/2022] [Indexed: 01/11/2023] Open
Abstract
Background Throughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which can lead to poor alignment and large gaps. This slows down computation and can impact conclusions without being biologically relevant. Cleaning the alignment by removing common issues such as gaps, divergent sequences, large insertions and deletions and poorly aligned sequence ends can substantially improve analyses. Manual editing of MSAs is very widespread but is time-consuming and difficult to reproduce. Results We present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed. The main functionalities of the tool include removing regions of low coverage due to insertions, removing gaps, cropping poorly aligned sequence ends and removing sequences that are too divergent or too short. The thresholds for each function can be specified by the user and parameters can be adjusted to each individual MSA. CIAlign is designed with an emphasis on solving specific and common alignment problems and on providing transparency to the user. Conclusion CIAlign effectively removes problematic regions and sequences from MSAs and provides novel visualisation options. This tool can be used to fine-tune alignments for further analysis and processing. The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way of visualising large MSAs.
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Affiliation(s)
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Laboury A, Bennion RF, Thuy B, Weis R, Fischer V. Anatomy and phylogenetic relationships of Temnodontosaurus zetlandicus (Reptilia: Ichthyosauria). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Parvipelvia is a major clade of ichthyosaurians that diversified during the Triassic-Jurassic transition. The interrelationships of early parvipelvians remain unclear and many genera are loosely diagnosed, such as Temnodontosaurus, an ecologically important genus from the Early Jurassic of Western Europe. One taxon concentrates many taxonomic issues: ‘Ichthyosaurus’ acutirostris was previously assigned to Temnodontosaurus and for which ‘Ichthyosaurus’ zetlandicus represents a junior synonym. We redescribe the holotype of ‘Ichthyosaurus’ zetlandicus (CAMSM J35176) and a new specimen probably attributable to this taxon (MNHNL TU885) from the Toarcian of Luxembourg. We find that Temnodontosaurus zetlandicus comb. nov. is a valid species that should be referred to the genus Temnodontosaurus, sharing a number of traits with Temnodontosaurus nuertingensis and Temnodontosaurus trigonodon, despite having a distinct cranial architecture. Our phylogenetic analyses under both implied weighting maximum parsimony and Bayesian inference recover T. zetlandicus as closely related to several species currently assigned to Temnodontosaurus. Species included in Temnodontosaurus form a polyphyletic yet well-clustered group among basal neoichthyosaurians, demonstrating that the monophyly of this genus needs to be thoroughly investigated.
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Affiliation(s)
- Antoine Laboury
- Evolution & Diversity Dynamics Lab, University of Liège, 14 Allée du 6 Août, Liège 4000, Belgium
| | - Rebecca F Bennion
- Evolution & Diversity Dynamics Lab, University of Liège, 14 Allée du 6 Août, Liège 4000, Belgium
- Palaeontology Department, Royal Belgian Institute of Natural Sciences, 29, Rue Vautier, 1000 Brussels, Belgium
| | - Ben Thuy
- Palaeontology Departement, Natural History Museum Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Grand-Duchy of Luxembourg
| | - Robert Weis
- Palaeontology Departement, Natural History Museum Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Grand-Duchy of Luxembourg
| | - Valentin Fischer
- Evolution & Diversity Dynamics Lab, University of Liège, 14 Allée du 6 Août, Liège 4000, Belgium
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Smith MR. Using information theory to detect rogue taxa and improve consensus trees. Syst Biol 2021; 71:1088-1094. [PMID: 34951650 PMCID: PMC9366444 DOI: 10.1093/sysbio/syab099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/29/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022] Open
Abstract
“Rogue” taxa of uncertain affinity can confound attempts to summarize the results of phylogenetic analyses. Rogues reduce resolution and support values in consensus trees, potentially obscuring strong evidence for relationships between other taxa. Information theory provides a principled means of assessing the congruence between a set of trees and their consensus, allowing rogue taxa to be identified more effectively than when using ad hoc measures of tree quality. A basic implementation of this approach in R recovers reduced consensus trees that are better resolved, more accurate, and more informative than those generated by existing methods. [Consensus trees; information theory; phylogenetic software; Rogue taxa.]
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Affiliation(s)
- Martin R Smith
- Department of Earth Sciences, Durham University, Lower Mountjoy, Durham, DH1 3LE, UK
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Yu YL, Li YD, Kolibáč J, Ślipiński A, Ren D, Pang H, Li ZQ. A New Genus and Species of Lophocateridae from Mid-Cretaceous Amber of Myanmar (Coleoptera). INSECTS 2021; 12:1052. [PMID: 34940140 PMCID: PMC8709423 DOI: 10.3390/insects12121052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
A new genus and species of the cleroid family Lophocateridae are described and illustrated from the mid-Cretaceous amber of northern Myanmar. Gracilenticrus burmiticus Yu, Kolibáč & Ślipiński gen. et sp. nov. is unique among Lophocateridae in the tiny body size, frontoclypeal suture and antennal grooves absent, symmetrical antennal clubs, protrochantin reduced, tarsal claws small and widened at base. A key to the species of Mesozoic Lophocateridae is also provided. Morphological characters of the newly discovered Gracilenticrus were analyzed together with representatives of 43 extant genera of Cleroidea (broadly defined Trogossitidae) in a matrix of 91 characters. Gracilenticrus burmiticus was resolved as a member of Lophocateridae. The discovery of a diverse fauna of Lophocateridae in the mid-Cretaceous sheds a new light on the early evolution of superfamily Cleroidea.
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Affiliation(s)
- Ya-Li Yu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China;
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China;
| | - Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Jiří Kolibáč
- Department of Entomology, Moravian Museum, Hviezdoslavova 29a, 62700 Brno, Czech Republic;
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia;
| | - Dong Ren
- College of Life Sciences, Capital Normal University, Beijing 100048, China;
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China;
| | - Zhi-Qiang Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China;
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Tube-dwelling in early animals exemplified by Cambrian scalidophoran worms. BMC Biol 2021; 19:243. [PMID: 34772414 PMCID: PMC8588615 DOI: 10.1186/s12915-021-01172-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background The radiation of ecdysozoans (moulting animals) during the Cambrian gave rise to panarthropods and various groups of worms including scalidophorans, which played an important role in the elaboration of early marine ecosystems. Although most scalidophorans were infaunal burrowers travelling through soft sediment at the bottom of the sea, Selkirkia lived inside a tube. Results We explore the palaeobiology of these tubicolous worms, and more generally the origin and evolutionary significance of tube-dwelling in early animals, based on exceptionally preserved fossils from the early Cambrian Chengjiang Lagerstätte (Stage 3, China) including a new species, Selkirkia transita sp. nov. We find that the best phylogenetic model resolves Selkirkia as a stem-group priapulid. Selkirkia secreted a protective cuticular thickening, the tube, inside which it was able to move during at least part of its life. Partly based on measured growth patterns, we construe that this tube was separated from the trunk during a moulting process that has no direct equivalent in other scalidophorans. Although the ontogeny of Selkirkia is currently unknown, we hypothesize that its conical tube might have had the same ecological function and possibly even deep development origin as the lorica, a protective cuticular thickening found in larval priapulids and adult loriciferans. Selkirkia is seen as a semi-sedentary animal capable of very shallow incursions below the water/sediment interface, possibly for feeding or during the tube-secreting phase. Brachiopod epibionts previously reported from the Xiaoshiba Lagerstätte (ca. 514 Ma) also presumably occur in Selkirkia sinica from Chengjiang (ca. 518 Ma). Conclusions Our critical and model-based approach provides a new phylogenetic framework for Scalidophora, upon which to improve in order to study the evolution of morphological characters in this group. Tube-dwelling is likely to have offered Selkirkia better protection and anchoring to sediment and has developed simultaneously in other Cambrian animals such as hemichordates, annelids or panarthropods. Often lost in modern representatives in favour of active infaunal lifestyles, tube-dwelling can be regarded as an early evolutionary response of various metazoans to increasing environmental and biological pressure in Cambrian marine ecosystems. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01172-4.
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Li Y, Tihelka E, Leschen RAB, Yu Y, Ślipiński A, Pang H, Huang D, Kolibáč J, Cai C. An exquisitely preserved tiny bark‐gnawing beetle (Coleoptera: Trogossitidae) from mid‐Cretaceous Burmese amber and the phylogeny of Trogossitidae. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan‐Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy Center for Excellence in Life and Paleoenvironment Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Nanjing China
| | - Erik Tihelka
- School of Earth Sciences University of Bristol Bristol UK
| | | | - Yali Yu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization Guangdong Public Laboratory of Wild Animal Conservation and Utilization Institute of Zoology Guangdong Academy of Sciences Guangzhou China
| | - Adam Ślipiński
- Australian National Insect Collection CSIRO Canberra ACT Australia
| | - Hong Pang
- State Key Laboratory of Biocontrol School of Ecology Sun Yat‐Sen University Guangzhou China
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy Center for Excellence in Life and Paleoenvironment Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Nanjing China
| | - Jiří Kolibáč
- Department of Entomology Moravian Museum Brno Czech Republic
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy Center for Excellence in Life and Paleoenvironment Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Nanjing China
- School of Earth Sciences University of Bristol Bristol UK
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Pastana MNL, Johnson GD, Datovo A. Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Abstract
More than half the ray-finned fishes and about one-quarter of all living vertebrates belong to Percomorphacea. Among its 30 orders, Stromateiformes encompass 77 species in 16 genera and six families. Stromateiform monophyly has never been tested using morphology, and it has been rejected by molecular analyses. This comprehensive revision of Stromateiformes includes all its valid genera of all percomorph families previously aligned with the order. We sampled 207 phenotypic characters in 66 terminal taxa representing 14 orders and 46 acanthopterygian families. This dataset significantly surpasses all previous phenotype-based phylogenies of Stromateiformes, which analysed only a fraction of these characters. Stromateiformes is recovered as monophyletic, supported by eight unequivocal synapomorphies. Amarsipidae is the sister group of all other Stromateiformes (= Stromateoidei). Centrolophidae is paraphyletic, with three of its genera allocated into an early-diverging clade and the other four appearing as successive sister groups to a lineage containing the remaining stromateiforms. All other stromateoid families are monophyletic, with the following cladistic arrangement: (Nomeidae (Stromateidae (Tetragonuridae, Ariommatidae))). Our analysis convincingly refutes recent molecular phylogenetic interpretations that fail to recover a monophyletic Stromateiformes. These findings call into question large-scale conclusions of percomorph relationships and trait evolution based solely on molecular data.
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Affiliation(s)
- Murilo N L Pastana
- Division of Fishes, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
| | - G David Johnson
- Division of Fishes, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Aléssio Datovo
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
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Echevarría LY, De la Riva I, Venegas PJ, Rojas-Runjaic FJM, R Dias I, Castroviejo-Fisher S. Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae). Cladistics 2021; 37:375-401. [PMID: 34478194 DOI: 10.1111/cla.12447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 01/06/2023] Open
Abstract
We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids and 127 outgroup terminals. We performed six analytical strategies combining different optimality criteria (parsimony and maximum likelihood), alignment methods (tree- and similarity-alignment), and three different indel coding schemes (fifth character state, unknown nucleotide, and presence/absence characters matrix). Furthermore, we analyzed a subset of the total evidence dataset to evaluate the impact of phenotypic characters on hemiphractid phylogenetic relationships. Our main results include: (i) monophyly of Hemiphractidae and its six genera for all our analyses, novel relationships among hemiphractid genera, and non-monophyly of Hemiphractinae according to our preferred phylogenetic hypothesis; (ii) non-monophyly of current supraspecific taxonomies of Gastrotheca, an updated taxonomy is provided; (iii) previous differences among studies were mainly caused by differences in analytical factors, not by differences in character/taxon sampling; (iv) optimality criteria, alignment method, and indel coding caused differences among optimal topologies, in that order of degree; (v) in most cases, parsimony analyses are more sensitive to the addition of phenotypic data than maximum likelihood analyses; (vi) adding phenotypic data resulted in an increase of shared clades for most analyses.
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Affiliation(s)
- Lourdes Y Echevarría
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.,División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Urb. Huertos de San Antonio, Santa Rita No. 105 Of. 202, Surco, Lima, Perú
| | - Ignacio De la Riva
- Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Pablo J Venegas
- División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Urb. Huertos de San Antonio, Santa Rita No. 105 Of. 202, Surco, Lima, Perú
| | | | - Iuri R Dias
- Graduate Program in Zoology, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, Ilhéus, Bahia, 45662-900, Brazil
| | - Santiago Castroviejo-Fisher
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.,Department of Herpetology, American Museum of Natural History, New York, NY, 10024, USA
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Asher RJ, Smith MR. Phylogenetic Signal and Bias in Paleontology. Syst Biol 2021; 71:986-1008. [PMID: 34469583 PMCID: PMC9248965 DOI: 10.1093/sysbio/syab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.
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Affiliation(s)
- Robert J Asher
- Department of Zoology, Downing St., University of Cambridge CB2 3EJ, UK
| | - Martin R Smith
- Department of Earth Sciences, Lower Mount Joy, Durham University, Durham DH1 3LE, UK
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López-Antoñanzas R, Peláez-Campomanes P. Bayesian Morphological Clock versus Parsimony: An insight into the relationships and dispersal events of postvacuum Cricetidae (Rodentia, Mammalia). Syst Biol 2021; 71:512-525. [PMID: 34297129 DOI: 10.1093/sysbio/syab059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/13/2021] [Accepted: 07/17/2021] [Indexed: 11/12/2022] Open
Abstract
Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only datasets. Herein, we present a morphological dataset for a group of cricetid rodents to which we apply an array of methods fairly new in palaeontology that can be used by palaeontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated and non-calibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our dataset, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes and diversification in cricetids.
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Affiliation(s)
- Raquel López-Antoñanzas
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), Université de Montpellier, Montpellier, France.,Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
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Lewin TD, Royall AH, Holland PWH. Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires. J Mol Evol 2021; 89:396-414. [PMID: 34097121 PMCID: PMC8208926 DOI: 10.1007/s00239-021-10012-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/11/2021] [Indexed: 11/21/2022]
Abstract
The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX, are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of a large tandem array of LEUTX loci in the genome of the European rabbit (Oryctolagus cuniculus). Despite extensive gene gain and loss, all sampled species possess at least two ETCHbox genes, suggesting their collective role is indispensable. We find evidence for positive selection and show that TPRX1 and TPRX2 have been the subject of repeated gene conversion across the Boreoeutheria, homogenising their sequences and preventing divergence, especially in the homeobox region. Together, these results are consistent with a model where mammalian ETCHbox genes are dynamic in evolution due to functional overlap, yet have collective indispensable roles.
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Affiliation(s)
- Thomas D Lewin
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Amy H Royall
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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Mongiardino Koch N, Garwood RJ, Parry LA. Fossils improve phylogenetic analyses of morphological characters. Proc Biol Sci 2021; 288:20210044. [PMID: 33947239 PMCID: PMC8246652 DOI: 10.1098/rspb.2021.0044] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth-death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.
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Affiliation(s)
| | - Russell J Garwood
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
- Earth Sciences Department, Natural History Museum, London, UK
| | - Luke A Parry
- Department of Earth Sciences, University of Oxford, Oxford, UK
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41
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Allman ES, Mitchell JD, Rhodes JA. Gene tree discord, simplex plots, and statistical tests under the coalescent. Syst Biol 2021; 71:929-942. [PMID: 33560348 DOI: 10.1093/sysbio/syab008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord, and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data is not in accord with the MSC, and thus that either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees is in accord with the MSC, the plots reveal when substantial incomplete lineage sorting is present. Applications to both simulated and empirical multilocus data sets illustrate the insights provided.
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Affiliation(s)
- Elizabeth S Allman
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99709, USA
| | - Jonathan D Mitchell
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99709, USA.,Unité Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | - John A Rhodes
- Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK 99709, USA
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42
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Varón-González C, Whelan S, Klingenberg CP. Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable. Syst Biol 2021; 69:863-883. [PMID: 31985800 DOI: 10.1093/sysbio/syaa003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/03/2020] [Accepted: 01/17/2020] [Indexed: 12/20/2022] Open
Abstract
In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny can be estimated reliably if dimensionality is high, even with relatively unfavorable combinations of branch lengths. By contrast, if there is phenotypic integration such that most variation is concentrated in one or a few dimensions, the reliability of phylogenetic estimates is severely reduced. Evolutionary models with stabilizing selection also produce highly unreliable estimates, which are little better than picking a phylogenetic tree at random. To examine how these results apply to phylogenies with more than four taxa, we conducted further simulations with up to eight taxa, which indicated that the effects of dimensionality and phenotypic integration extend to more than four taxa, and that convergence among internal nodes may produce additional complications specifically for greater numbers of taxa. Overall, the simulations suggest that multidimensional data, under evolutionary models that are plausible for biological data, do not produce reliable estimates of phylogeny. [Brownian motion; gene expression data; geometric morphometrics; morphological integration; squared-change parsimony; phylogeny; shape; stabilizing selection.].
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Affiliation(s)
- Ceferino Varón-González
- School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon Whelan
- School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.,Department of Evolutionary Biology, EBC, Uppsala University, Norbyägen 18D, 75236 Uppsala, Sweden
| | - Christian Peter Klingenberg
- School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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43
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Machado M, Teixeira RA. Phylogenetic relationships in Stephanopinae: systematics of Stephanopis and Sidymella based on morphological characters (Araneae: Thomisidae). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-020-00472-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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44
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Bossert S, Murray EA, Pauly A, Chernyshov K, Brady SG, Danforth BN. Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees. Syst Biol 2020; 70:803-821. [PMID: 33367855 DOI: 10.1093/sysbio/syaa097] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 11/12/2022] Open
Abstract
Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree, and RAxML. We study their performance in the phylogenomic framework of $>$800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus Pseudapis, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (ModelFinder program). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for Pseudapis s. l. and map the distribution of distinct morphological features of the group. [ASTRAL; Bees; concordance; gene tree estimation error; IQ-Tree; MrBayes, Nomiinae; PhyloBayes; RAxML; phylogenomics; stemminess].
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, Washington State University, Pullman, Washington 99164, USA
| | - Elizabeth A Murray
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Department of Entomology, Washington State University, Pullman, Washington 99164, USA
| | - Alain Pauly
- O.D. Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000 Brussels, Belgium
| | - Kyrylo Chernyshov
- College of Arts and Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA
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45
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Fischer V, Zverkov NG, Arkhangelsky MS, Stenshin IM, Blagovetshensky IV, Uspensky GN. A new elasmosaurid plesiosaurian from the Early Cretaceous of Russia marks an early attempt at neck elongation. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Plesiosaurian marine reptiles evolved a wide range of body shapes during the Jurassic and Cretaceous, including long-necked forms. Many Late Cretaceous members of the clade Elasmosauridae epitomized this part of the plesiosaurian morphological spectrum by evolving extremely long necks through somitogenesis (resulting in an increase in the number of cervical centra) and differential growth (resulting in the elongation of cervical centra). However, the early evolution of elasmosaurids remains poorly understood because of a generally poor Lower Cretaceous fossil record. We describe a new elasmosaurid, Jucha squalea gen. et sp. nov., from the upper Hauterivian (Lower Cretaceous) of Ulyanovsk (European Russia), in addition to other elasmosaurid remains from the same area. Jucha squalea is one of the oldest and basalmost elasmosaurids known and lacks a series of features that otherwise characterize the group, such as the heart-shaped intercoracoid fenestra and the median pectoral bar. However, Jucha squalea marks an early attempt at cervical elongation through differential growth. The data we gathered on the shape of cervical centra among elasmosaurids suggest multiple episodes of elongation and shortening. However, the precise patterns are obscured by an unstable phylogenetic signal.
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Affiliation(s)
- Valentin Fischer
- Evolution & Diversity Dynamics Lab, Université de Liège, Allée du 6 Août, Liège, Belgium
| | - Nikolay G Zverkov
- Borissiak Paleontological Institute of the Russian Academy of Sciences, Moscow, Russia
- Geological Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Maxim S Arkhangelsky
- Department of General Geology and Minerals, Saratov State University, Saratov, Russia
- Department of Geoecology and Engineering Geology, Saratov State Technical University, Saratov, Russia
| | - Ilya M Stenshin
- Undory Paleontological Museum, Undory, Ulyanovsk Region, Russia
| | - Ivan V Blagovetshensky
- Department of Biology, Ecology and Nature Management, Ulyanovsk State University, Ulyanovsk, Russia
| | - Gleb N Uspensky
- Natural Science Museum, Ulyanovsk State University, Ulyanovsk, Russia
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46
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Keating JN, Sansom RS, Sutton MD, Knight CG, Garwood RJ. Morphological Phylogenetics Evaluated Using Novel Evolutionary Simulations. Syst Biol 2020; 69:897-912. [PMID: 32073641 PMCID: PMC7440746 DOI: 10.1093/sysbio/syaa012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/31/2020] [Accepted: 02/07/2020] [Indexed: 02/04/2023] Open
Abstract
Evolutionary inferences require reliable phylogenies. Morphological data have traditionally been analyzed using maximum parsimony, but recent simulation studies have suggested that Bayesian analyses yield more accurate trees. This debate is ongoing, in part, because of ambiguity over modes of morphological evolution and a lack of appropriate models. Here, we investigate phylogenetic methods using two novel simulation models-one in which morphological characters evolve stochastically along lineages and another in which individuals undergo selection. Both models generate character data and lineage splitting simultaneously: the resulting trees are an emergent property, rather than a fixed parameter. Standard consensus methods for Bayesian searches (Mki) yield fewer incorrect nodes and quartets than the standard consensus trees recovered using equal weighting and implied weighting parsimony searches. Distances between the pool of derived trees (most parsimonious or posterior distribution) and the true trees-measured using Robinson-Foulds (RF), subtree prune and regraft (SPR), and tree bisection reconnection (TBR) metrics-demonstrate that this is related to the search strategy and consensus method of each technique. The amount and structure of homoplasy in character data differ between models. Morphological coherence, which has previously not been considered in this context, proves to be a more important factor for phylogenetic accuracy than homoplasy. Selection-based models exhibit relatively lower homoplasy, lower morphological coherence, and higher inaccuracy in inferred trees. Selection is a dominant driver of morphological evolution, but we demonstrate that it has a confounding effect on numerous character properties which are fundamental to phylogenetic inference. We suggest that the current debate should move beyond considerations of parsimony versus Bayesian, toward identifying modes of morphological evolution and using these to build models for probabilistic search methods. [Bayesian; evolution; morphology; parsimony; phylogenetics; selection; simulation.].
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Affiliation(s)
- Joseph N Keating
- Department of Earth and Environmental Sciences, Universityof Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Robert S Sansom
- Department of Earth and Environmental Sciences, Universityof Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | - Mark D Sutton
- Department of Earth Science and Engineering, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Christopher G Knight
- Department of Earth and Environmental Sciences, Universityof Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | - Russell J Garwood
- Department of Earth and Environmental Sciences, Universityof Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
- Earth Sciences Department, Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
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47
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King B. Bayesian Tip-Dated Phylogenetics in Paleontology: Topological Effects and Stratigraphic Fit. Syst Biol 2020; 70:283-294. [PMID: 32692834 DOI: 10.1093/sysbio/syaa057] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/14/2022] Open
Abstract
The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several data sets with multiple phylogenetic methods, that topologies produced by tip dating are outliers as compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio (GER) and the Stratigraphic Completeness Index (SCI). This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favors tree topologies with high stratigraphic fit metrics is modulated by the diversification dynamics of the group under investigation. In particular, when net diversification rate is low, the tree model favors trees with a higher GER compared to when net diversification rate is high. Differences in stratigraphic fit and tree topology between tip dating and other methods are concentrated in parts of the tree with weaker character signal, as shown by successive deletion of the most incomplete taxa from two data sets. These results show that tip dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit an expectation that can be overturned by strong evidence from character data. [fossilized birth-death; fossils; missing data; morphological clock; morphology; parsimony; phylogenetics.].
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Affiliation(s)
- Benedict King
- Naturalis Biodiversity Center, Postbus 9517, 2300 RA, Leiden, The Netherlands.,College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
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48
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Smith MR. Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees. Bioinformatics 2020; 36:5007-5013. [DOI: 10.1093/bioinformatics/btaa614] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 06/03/2020] [Accepted: 06/26/2020] [Indexed: 11/15/2022] Open
Abstract
Abstract
Motivation
The Robinson–Foulds (RF) metric is widely used by biologists, linguists and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies the number of bipartition splits that occur in both trees—but this conservative approach ignores potential similarities between almost-identical splits, with undesirable consequences. ‘Generalized’ RF metrics address this shortcoming by pairing splits in one tree with similar splits in the other. Each pair is assigned a similarity score, the sum of which enumerates the similarity between two trees. The challenge lies in quantifying split similarity: existing definitions lack a principled statistical underpinning, resulting in misleading tree distances that are difficult to interpret. Here, I propose probabilistic measures of split similarity, which allow tree similarity to be measured in natural units (bits).
Results
My new information-theoretic metrics outperform alternative measures of tree similarity when evaluated against a broad suite of criteria, even though they do not account for the non-independence of splits within a single tree. Mutual clustering information exhibits none of the undesirable properties that characterize other tree comparison metrics, and should be preferred to the RF metric.
Availability and implementation
The methods discussed in this article are implemented in the R package ‘TreeDist’, archived at https://dx.doi.org/10.5281/zenodo.3528123.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin R Smith
- Department of Earth Sciences, Lower Mountjoy, Durham University, Durham DH1 3LE, UK
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49
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Koch NM, Parry LA. Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses. Syst Biol 2020; 69:1052-1067. [DOI: 10.1093/sysbio/syaa023] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred using only data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes (such as ancestral states, paleobiogeography and diversification dynamics), the role fossils play in reconstructing phylogeny is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. Incorporating fossils often (yet not always) induces stronger topological changes than increasing sampling of extant taxa. Fossils also produce unique topological rearrangements, allowing the exploration of regions of treespace that are never visited by analyses of only extant taxa. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any phylogenetic analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses. [phylogeny, morphology, fossils, parsimony, Bayesian inference.]
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06510, USA
| | - Luke A Parry
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06510, USA
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50
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Groh SS, Upchurch P, Barrett PM, Day JJ. The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.
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Affiliation(s)
- Sebastian S Groh
- Department of Earth Sciences, University College London, London, UK
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Paul Upchurch
- Department of Earth Sciences, University College London, London, UK
| | - Paul M Barrett
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Julia J Day
- Department of Genetics, Environment and Evolution, University College London, London, UK
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