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Cho A, Lax G, Keeling PJ. Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages. Mol Phylogenet Evol 2024:108120. [PMID: 38852907 DOI: 10.1016/j.ympev.2024.108120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
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2
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Gupta A, Mirarab S, Turakhia Y. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596098. [PMID: 38854139 PMCID: PMC11160643 DOI: 10.1101/2024.05.27.596098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.
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Affiliation(s)
- Anshu Gupta
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
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3
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Lähteenaro M, Benda D, Straka J, Nylander JAA, Bergsten J. Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees. Mol Phylogenet Evol 2024; 195:108068. [PMID: 38554985 DOI: 10.1016/j.ympev.2024.108068] [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: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.
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Affiliation(s)
- Meri Lähteenaro
- Department of Zoology, Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Faculty of Science, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Daniel Benda
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44, Prague 2, Czech Republic; Department of Entomology, National Museum of the Czech Republic, Cirkusová 1740, CZ-19300 Prague 9, Czech Republic.
| | - Jakub Straka
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44, Prague 2, Czech Republic.
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-106 91 Stockholm, Sweden.
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Faculty of Science, Stockholm University, SE-106 91 Stockholm, Sweden.
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Schultz DT, Heath-Heckman EA, Winchell CJ, Kuo DH, Yu YS, Oberauer F, Kocot KM, Cho SJ, Simakov O, Weisblat DA. Acceleration of genome rearrangement in clitellate annelids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593736. [PMID: 38798472 PMCID: PMC11118384 DOI: 10.1101/2024.05.12.593736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.
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Affiliation(s)
- Darrin T. Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Elizabeth A.C. Heath-Heckman
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Christopher J. Winchell
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| | - Dian-Han Kuo
- Department of Life Science & Museum of Zoology, National Taiwan University, No. 1 Section 4 Roosevelt Rd., Taipei 10617, Taiwan
| | - Yun-sang Yu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Fabian Oberauer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - David A. Weisblat
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
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Yap-Chiongco MK, Bergmeier FS, Roberts NG, Jörger KM, Kocot KM. Phylogenomic reconstruction of Solenogastres (Mollusca, Aplacophora) informs hypotheses on body size evolution. Mol Phylogenet Evol 2024; 194:108029. [PMID: 38341006 DOI: 10.1016/j.ympev.2024.108029] [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: 10/18/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Body size is a fundamental characteristic of animals that impacts every aspect of their biology from anatomical complexity to ecology. In Mollusca, Solenogastres has been considered important to understanding the group's early evolution as most morphology-based phylogenetic reconstructions placed it as an early branching molluscan lineage. Under this scenario, molluscs were thought to have evolved from a small, turbellarian-like ancestor and small (i.e., macrofaunal) body size was inferred to be plesiomorphic for Solenogastres. More recently, phylogenomic studies have shown that aplacophorans (Solenogastres + Caudofoveata) form a clade with chitons (Polyplacophora), which is sister to all other molluscs, suggesting a relatively large-bodied (i.e., megafaunal) ancestor for Mollusca. Meanwhile, recent investigations into aplacophoran phylogeny have called the assumption that the last common ancestor of Solenogastres was small-bodied into question, but sampling of meiofaunal species was limited, biasing these studies towards large-bodied taxa and leaving fundamental questions about solenogaster body size evolution unanswered. Here, we supplemented available data with transcriptomes from eight diverse meiofaunal species of Solenogastres and conducted phylogenomic analyses on datasets of up to 949 genes. Maximum likelihood analyses support the meiofaunal family Meiomeniidae as the sister group to all other solenogasters, congruent with earlier ideas of a small-bodied ancestor of Solenogastres. In contrast, Bayesian Inference analyses support the large-bodied family Amphimeniidae as the sister group to all other solenogasters. Investigation of phylogenetic signal by comparing site-wise likelihood scores for the two competing hypotheses support the Meiomeniidae-first topology. In light of these results, we performed ancestral character state reconstruction to explore the implications of both hypotheses on understanding of Solenogaster evolution and review previous hypotheses about body size evolution and its potential consequences for solenogaster biology. Both hypotheses imply that body size evolution has been highly dynamic over the course of solenogaster evolution and that their relatively static body plan has successfully allowed for evolutionary transitions between meio-, macro- and megafaunal size ranges.
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Affiliation(s)
| | | | - Nickellaus G Roberts
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Katharina M Jörger
- SNSB-Bavarian State Collection for Zoology, Section Mollusca, Munich, Germany
| | - Kevin M Kocot
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA; Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, AL, USA.
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Fedosov AE, Zaharias P, Lemarcis T, Modica MV, Holford M, Oliverio M, Kantor YI, Puillandre N. Phylogenomics of Neogastropoda: the backbone hidden in the bush. Syst Biol 2024:syae010. [PMID: 38456663 DOI: 10.1093/sysbio/syae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Indexed: 03/09/2024] Open
Abstract
The molluscan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in early stages of diversification, generating a 'bush' at the base of their evolutionary tree, that has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1,817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, three prove problematic: First, uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade, or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major 'core Neogastropoda' grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analysed phylogenetic signal of targeted loci in relation to potential biases, and we propose most probable resolutions in the latter two recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci.
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Affiliation(s)
- Alexander E Fedosov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Thomas Lemarcis
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Maria Vittoria Modica
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Mandë Holford
- Department of Chemistry, Hunter College, Belfer Research Building, City University of New York, New York, USA
- Department of Invertebrate Zoology, the American Museum of Natural History, New York, USA
- PhD programs in Biology, Biochemistry, and Chemistry, The Graduate Center of the City University of New York, New York, USA
| | - Marco Oliverio
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome. Zoology, Rome, Italy
| | - Yuri I Kantor
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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7
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Lin YT, Ip JCH, He X, Gao ZM, Perez M, Xu T, Sun J, Qian PY, Qiu JW. Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration. THE ISME JOURNAL 2024; 18:wrae048. [PMID: 38531780 PMCID: PMC10999363 DOI: 10.1093/ismejo/wrae048] [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: 02/13/2024] [Revised: 03/06/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024]
Abstract
Previous studies have revealed tight metabolic complementarity between bivalves and their endosymbiotic chemosynthetic bacteria, but little is known about their interactions with ectosymbionts. Our analysis of the ectosymbiosis between a deep-sea scallop (Catillopecten margaritatus) and a gammaproteobacterium showed that bivalves could be highly interdependent with their ectosymbionts as well. Our microscopic observation revealed abundant sulfur-oxidizing bacteria (SOB) on the surfaces of the gill epithelial cells. Microbial 16S rRNA gene amplicon sequencing of the gill tissues showed the dominance of the SOB. An analysis of the SOB genome showed that it is substantially smaller than its free-living relatives and has lost cellular components required for free-living. Genomic and transcriptomic analyses showed that this ectosymbiont relies on rhodanese-like proteins and SOX multienzyme complex for energy generation, mainly on the Calvin-Benson-Bassham (CBB) cycle and peripherally on a phosphoenolpyruvate carboxylase for carbon assimilation. Besides, the symbiont encodes an incomplete tricarboxylic acid (TCA) cycle. Observation of the scallop's digestive gland and its nitrogen metabolism pathways indicates it does not fully rely on the ectosymbiont for nutrition. Analysis of the host's gene expression provided evidence that it could offer intermediates for the ectosymbiont to complete its TCA cycle and some amino acid synthesis pathways using exosomes, and its phagosomes, endosomes, and lysosomes might be involved in harvesting nutrients from the symbionts. Overall, our study prompts us to rethink the intimacy between the hosts and ectosymbionts in Bivalvia and the evolution of chemosymbiosis in general.
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Affiliation(s)
- Yi-Tao Lin
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, 999077, China
| | - Jack Chi-Ho Ip
- Science Unit, Lingnan University, Hong Kong SAR, 999077, China
| | - Xing He
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Zhao-Ming Gao
- Deep-sea Science Division, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Maeva Perez
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, 999077, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, 999077, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, 999077, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, 999077, China
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Qi Y, Zhong Z, Liu X, He X, Zhou Y, Zhang L, Chen C, Linse K, Qiu JW, Sun J. Phylogenomic analyses reveal a single deep-water colonisation in Patellogastropoda. Mol Phylogenet Evol 2024; 190:107968. [PMID: 38000707 DOI: 10.1016/j.ympev.2023.107968] [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: 09/27/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Patellogastropoda, the true limpets, is a major group of gastropods widely distributed in marine habitats from the intertidal to deep sea. Though important for understanding their evolutionary radiation, the phylogenetic relationships among the patellogastropod families have always been challenging to reconstruct, with contradictory results likely due to insufficient sampling. Here, we obtained mitogenomic and phylogenomic data (transcriptomic or genomic) from six species representing the three predominantly deep-water patellogastropod families: Lepetidae, Neolepetopsidae, and Pectinodontidae. By using various phylogenetic methods, we show that mitogenome phylogeny recovers monophyly of eight families in most of the trees, though the relationships among families remain contentious. Meanwhile, a more robust family-level topology consistent with morphology was achieved by phylogenomics. This also reveals that these mainly deep-water families are monophyletic, suggesting a single colonisation of the deep water around the Jurassic. We also found a lack of significant correlation between genome size and habitat depth, despite some deep-water species exhibiting larger genome sizes. Our phylogenomic tree provides a stable phylogenetic backbone for Patellogastropoda that includes seven of the nine recognized families and paves the way for future evolutionary analyses in this major group of molluscs.
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Affiliation(s)
- Ying Qi
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Zhaoyan Zhong
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Xu Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Xing He
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 311005, China
| | - Lili Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Katrin Linse
- British Antarctic Survey, Cambridge, United Kingdom
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Jin Sun
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China.
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Gainett G, Klementz BC, Setton EVW, Simian C, Iuri HA, Edgecombe GD, Peretti AV, Sharma PP. A plurality of morphological characters need not equate with phylogenetic accuracy: A rare genomic change refutes the placement of Solifugae and Pseudoscorpiones in Haplocnemata. Evol Dev 2023:e12467. [PMID: 38124251 DOI: 10.1111/ede.12467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Recent advances in higher-level invertebrate phylogeny have leveraged shared features of genomic architecture to resolve contentious nodes across the tree of life. Yet, the interordinal relationships within Chelicerata have remained recalcitrant given competing topologies in recent molecular analyses. As such, relationships between topologically unstable orders remain supported primarily by morphological cladistic analyses. Solifugae, one such unstable chelicerate order, has long been thought to be the sister group of Pseudoscorpiones, forming the clade Haplocnemata, on the basis of eight putative morphological synapomorphies. The discovery, however, of a shared whole genome duplication placing Pseudoscorpiones in Arachnopulmonata provides the opportunity for a simple litmus test evaluating the validity of Haplocnemata. Here, we present the first developmental transcriptome of a solifuge (Titanopuga salinarum) and survey copy numbers of the homeobox genes for evidence of systemic duplication. We find that over 70% of the identified homeobox genes in T. salinarum are retained in a single copy, while representatives of the arachnopulmonates retain orthologs of those genes as two or more copies. Our results refute the placement of Solifugae in Haplocnemata. Subsequent reevaluation of putative interordinal morphological synapomorphies among chelicerates reveals a high incidence of homoplasy, reversals, and inaccurate coding within Haplocnemata and other small clades, as well as Arachnida more broadly, suggesting existing morphological character matrices are insufficient to resolve chelicerate phylogeny.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin C Klementz
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Catalina Simian
- Departamento de Diversidad Biológica y Ecología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Laboratorio de Biología Reproductiva y Evolución, Consejo Nacional de Investigaciones Científicas Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Hernán A Iuri
- División de Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Gregory D Edgecombe
- Department of Earth Sciences, Division ES Invertebrates and Plants Palaeobiology, The Natural History Museum, London, UK
| | - Alfredo V Peretti
- Departamento de Diversidad Biológica y Ecología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Laboratorio de Biología Reproductiva y Evolución, Consejo Nacional de Investigaciones Científicas Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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10
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Santibáñez-López CE, Ojanguren-Affilastro AA, Graham MR, Sharma PP. Congruence between ultraconserved element-based matrices and phylotranscriptomic datasets in the scorpion Tree of Life. Cladistics 2023; 39:533-547. [PMID: 37401727 DOI: 10.1111/cla.12551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2023] [Indexed: 07/05/2023] Open
Abstract
Scorpions are ancient and historically renowned for their potent venom. Traditionally, the systematics of this group of arthropods was supported by morphological characters, until recent phylogenomic analyses (using RNAseq data) revealed most of the higher-level taxa to be non-monophyletic. While these phylogenomic hypotheses are stable for almost all lineages, some nodes have been hard to resolve due to minimal taxonomic sampling (e.g. family Chactidae). In the same line, it has been shown that some nodes in the Arachnid Tree of Life show disagreement between hypotheses generated using transcritptomes and other genomic sources such as the ultraconserved elements (UCEs). Here, we compared the phylogenetic signal of transcriptomes vs. UCEs by retrieving UCEs from new and previously published scorpion transcriptomes and genomes, and reconstructed phylogenies using both datasets independently. We reexamined the monophyly and phylogenetic placement of Chactidae, sampling an additional chactid species using both datasets. Our results showed that both sets of genome-scale datasets recovered highly similar topologies, with Chactidae rendered paraphyletic owing to the placement of Nullibrotheas allenii. As a first step toward redressing the systematics of Chactidae, we establish the family Anuroctonidae (new family) to accommodate the genus Anuroctonus.
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Affiliation(s)
| | | | - Matthew R Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, 06226, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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11
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Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nat Rev Genet 2023; 24:834-850. [PMID: 37369847 DOI: 10.1038/s41576-023-00620-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.
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Affiliation(s)
- Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
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12
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Wang W, Dong Z, Du Z, Wu P. Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias. Mol Phylogenet Evol 2023; 189:107924. [PMID: 37699449 DOI: 10.1016/j.ympev.2023.107924] [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: 05/17/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/14/2023]
Abstract
Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zequn Dong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengxiang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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13
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Romeiro-Brito M, Taylor NP, Zappi DC, Telhe MC, Franco FF, Moraes EM. Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing. ANNALS OF BOTANY 2023; 132:989-1006. [PMID: 37815357 PMCID: PMC10808018 DOI: 10.1093/aob/mcad153] [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: 05/20/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND AND AIMS Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe. METHODS We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches. KEY RESULTS Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae. CONCLUSIONS We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, Gibraltar
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas Universidade de Brasília (UNB), Brasília, Distrito Federal, Brazil
| | - Milena C Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Fernando F Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
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14
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Liu X, Sigwart JD, Sun J. Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell-eye evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:525-537. [PMID: 38045544 PMCID: PMC10689665 DOI: 10.1007/s42995-023-00207-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 11/01/2023] [Indexed: 12/05/2023]
Abstract
Mollusca is the second-largest animal phylum with over 100,000 extant species representing eight classes. Across 1000 extant species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess "shell eyes", i.e., true eyes with a lens and retina that are embedded within the dorsal shells. The phylogeny of the major chiton clades is mostly well established, in a set of superfamily-level and higher level taxa supported by various approaches, including morphological studies, multiple gene markers, mitogenome-phylogeny, and phylotranscriptomic approaches. However, one critical lineage has remained unclear, namely Schizochiton which was controversially suggested as being the potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assemblies of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. We found that phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. However, a consistent and robust topology was generated with protein-coding genes using different models and methods. Our results support Schizochitonoidea as the sister group to other Chitonoidea in Chitonina, in agreement with the established classification. Combined with evidence from fossils, our phylogenetic results suggest that the earliest origin of shell eyes is in Schizochitonoidea, and that these structures were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding of the evolution of Polyplacophora.
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Affiliation(s)
- Xu Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
| | - Julia D. Sigwart
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt Am Main, Germany
| | - Jin Sun
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
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15
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Kelly MBJ, Khan MK, Wierucka K, Jones BR, Shofner R, Derkarabetian S, Wolff JO. Dynamic evolution of locomotor performance independent of changes in extended phenotype use in spiders. Proc Biol Sci 2023; 290:20232035. [PMID: 37876190 PMCID: PMC10598421 DOI: 10.1098/rspb.2023.2035] [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: 05/03/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Many animals use self-built structures (extended phenotypes) to enhance body functions, such as thermoregulation, prey capture or defence. Yet, it is unclear whether the evolution of animal constructions supplements or substitutes body functions-with disparate feedbacks on trait evolution. Here, using brown spiders (Araneae: marronoid clade), we explored if the evolutionary loss and gain of silken webs as extended prey capture devices correlates with alterations in traits known to play an important role in predatory strikes-locomotor performance (sprint speed) and leg spination (expression of capture spines on front legs). We found that in this group high locomotor performance, with running speeds of over 100 body lengths per second, evolved repeatedly-both in web-building and cursorial spiders. There was no correlation with running speed, and leg spination only poorly correlated, relative to the use of extended phenotypes, indicating that web use does not reduce selective pressures on body functions involved in prey capture and defence per se. Consequently, extended prey capture devices serve as supplements rather than substitutions to body traits and may only be beneficial in conjunction with certain life-history traits, possibly explaining the rare evolution and repeated loss of trapping strategies in predatory animals.
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Affiliation(s)
- Michael B. J. Kelly
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Md Kawsar Khan
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195 Berlin, Germany
| | - Kaja Wierucka
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Behavioural Ecology and Sociobiology Unit, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Braxton R. Jones
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- School of Biological Sciences, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Ryan Shofner
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences E26, University of New South Wales, Sydney 2052, Australia
| | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Jonas O. Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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16
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Aristide L, Fernández R. Genomic Insights into Mollusk Terrestrialization: Parallel and Convergent Gene Family Expansions as Key Facilitators in Out-of-the-Sea Transitions. Genome Biol Evol 2023; 15:evad176. [PMID: 37793176 PMCID: PMC10581543 DOI: 10.1093/gbe/evad176] [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: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in mollusks, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine ∼100 genomic data sets encompassing all major molluskan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question) and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to nonmarine habitats, highlighting the relevance of the preexisting genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution-parallelism, convergence, and innovation-can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluskan terrestrialization that paves the way toward further understanding the functional and evolutionary bases of this process.
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Affiliation(s)
- Leandro Aristide
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
| | - Rosa Fernández
- Metazoa Phylogenomics Laboratory Biodiversity Program, Institute of Evolutionary Biology (Spanish Research Council-University Pompeu Fabra), BarcelonaSpain
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17
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Song H, Wang Y, Shao H, Li Z, Hu P, Yap-Chiongco MK, Shi P, Zhang T, Li C, Wang Y, Ma P, Vinther J, Wang H, Kocot KM. Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting. Proc Natl Acad Sci U S A 2023; 120:e2302361120. [PMID: 37738291 PMCID: PMC10556646 DOI: 10.1073/pnas.2302361120] [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: 02/13/2023] [Accepted: 08/18/2023] [Indexed: 09/24/2023] Open
Abstract
The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella, Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.
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Affiliation(s)
- Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Haojing Shao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuoqing Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Pinli Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | | | - Pu Shi
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Tao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Cui Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yiguan Wang
- Institute of Ecology and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Peizhen Ma
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jakob Vinther
- School of Biological Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
- School of Earth Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - Haiyan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL35487
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL35487
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18
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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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19
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Fleming J, Eriksen PM, Struck TH. Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric. F1000Res 2023; 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: 08/01/2023] [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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20
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Bernot JP, Owen CL, Wolfe JM, Meland K, Olesen J, Crandall KA. Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling. Mol Biol Evol 2023; 40:msad175. [PMID: 37552897 PMCID: PMC10414812 DOI: 10.1093/molbev/msad175] [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: 10/30/2022] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 08/10/2023] Open
Abstract
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.
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Affiliation(s)
- James P Bernot
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, ℅ National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kenneth Meland
- Department of Biology, University of Bergen, Bergen, Norway
| | - Jørgen Olesen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Keith A Crandall
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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21
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Mongiardino Koch N, Tilic E, Miller AK, Stiller J, Rouse GW. Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea. Proc Biol Sci 2023; 290:20230988. [PMID: 37434530 PMCID: PMC10336381 DOI: 10.1098/rspb.2023.0988] [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: 05/02/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest oceanic trenches. Their reduced skeletons and limited number of phylogenetically informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with 13 novel transcriptomes. Using a highly curated dataset of 1100 orthologues, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favour one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories.
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Affiliation(s)
| | - Ekin Tilic
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Marine Zoology, Senckenberg Research Institute and Museum, Frankfurt, Germany
| | - Allison K. Miller
- Anatomy Department, University of Otago, Dunedin, Otago, New Zealand
| | - Josefin Stiller
- Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Greg W. Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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22
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Gardner EM, Bruun-Lund S, Niissalo M, Chantarasuwan B, Clement WL, Geri C, Harrison RD, Hipp AL, Holvoet M, Khew G, Kjellberg F, Liao S, Pederneiras LC, Peng YQ, Pereira JT, Phillipps Q, Ahmad Puad AS, Rasplus JY, Sang J, Schou SJ, Velautham E, Weiblen GD, Zerega NJC, Zhang Q, Zhang Z, Baraloto C, Rønsted N. Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs. Proc Natl Acad Sci U S A 2023; 120:e2222035120. [PMID: 37399402 PMCID: PMC10334730 DOI: 10.1073/pnas.2222035120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/11/2023] [Indexed: 07/05/2023] Open
Abstract
Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.
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Affiliation(s)
- Elliot M. Gardner
- International Center for Tropical Botany at the Kampong, Institute of Environment, Florida International University, Miami, FL33133
- National Tropical Botanical Garden, Kalāheo, HI96741
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - Sam Bruun-Lund
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
| | - Matti Niissalo
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - Bhanumas Chantarasuwan
- Thailand National History Museum, National Science Museum, Klong Luang, Pathum Thani12120, Thailand
| | - Wendy L. Clement
- Department of Biology, The College of New Jersey, Ewing, NJ08618
| | - Connie Geri
- Sarawak Forestry Corporation, 93250Kuching, Sarawak, Malaysia
| | | | | | - Maxime Holvoet
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
| | - Gillian Khew
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - Finn Kjellberg
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, 34090Montpellier, France
| | - Shuai Liao
- The Morton Arboretum, Lisle, IL60532
- South China Botanical Garden, Chinese Academy of Sciences, 510650Guangzhou, China
- School of Life Sciences, East China Normal University, 200241Shanghai, China
| | - Leandro Cardoso Pederneiras
- Instituto de Pesquisa do Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, 22460-030Rio de Janeiro–RJ, Brazil
| | - Yan-Qiong Peng
- Chinese Academy of Sciences, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303Mengla, China
| | - Joan T. Pereira
- Sabah Forest Research Centre, Sabah Forestry Department, 90175Sandakan, Sabah, Malaysia
| | | | - Aida Shafreena Ahmad Puad
- Faculty of Agriculture & Applied Sciences, i-CATS University College, 93350Kuching, Sarawak, Malaysia
| | - Jean-Yves Rasplus
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 34988Montpellier, France
| | - Julia Sang
- Sarawak Forest Department, 34988Kuching, Sarawak, Malaysia
| | - Sverre Juul Schou
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
| | - Elango Velautham
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - George D. Weiblen
- Bell Museum, University of Minnesota, St. Paul, MN55113
- Department of Plant Biology, University of Minnesota, St. Paul, MN55108
| | - Nyree J. C. Zerega
- Plant Biology and Conservation, Northwestern University, Evanston, IL60208
- Negaunee Institute for Plant Conservation and Action, Chicago Botanic Garden, Glencoe, IL60022
| | - Qian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093Beijing, China
| | - Zhen Zhang
- School of Life Sciences, East China Normal University, 200241Shanghai, China
| | - Christopher Baraloto
- International Center for Tropical Botany at the Kampong, Institute of Environment, Florida International University, Miami, FL33133
| | - Nina Rønsted
- National Tropical Botanical Garden, Kalāheo, HI96741
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
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23
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Balart-García P, Aristide L, Bradford TM, Beasley-Hall PG, Polak S, Cooper SJB, Fernández R. Parallel and convergent genomic changes underlie independent subterranean colonization across beetles. Nat Commun 2023; 14:3842. [PMID: 37386018 PMCID: PMC10310748 DOI: 10.1038/s41467-023-39603-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/21/2023] [Indexed: 07/01/2023] Open
Abstract
Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying cave-related phenotypes are largely unexplored from a macroevolutionary perspective. Here we investigate genome-wide gene evolutionary dynamics in three distantly related beetle tribes with at least six instances of independent colonization of subterranean habitats, inhabiting both aquatic and terrestrial underground systems. Our results indicate that remarkable gene repertoire changes mainly driven by gene family expansions occurred prior to underground colonization in the three tribes, suggesting that genomic exaptation may have facilitated a strict subterranean lifestyle parallelly across beetle lineages. The three tribes experienced both parallel and convergent changes in the evolutionary dynamics of their gene repertoires. These findings pave the way towards a deeper understanding of the evolution of the genomic toolkit in hypogean fauna.
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Affiliation(s)
- Pau Balart-García
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| | - Leandro Aristide
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Tessa M Bradford
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Perry G Beasley-Hall
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Slavko Polak
- Notranjska Museum Postojna, Kolodvorska c. 3, 6230, Postojna, Slovenia
| | - Steven J B Cooper
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Rosa Fernández
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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24
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Abalde S, Crocetta F, Tenorio MJ, D'Aniello S, Fassio G, Rodríguez-Flores PC, Uribe JE, M L Afonso C, Oliverio M, Zardoya R. Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus. Mol Phylogenet Evol 2023:107838. [PMID: 37286063 DOI: 10.1016/j.ympev.2023.107838] [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: 10/06/2022] [Revised: 05/15/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Fabio Crocetta
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Paula C Rodríguez-Flores
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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25
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Zhao M, Kurtis SM, White ND, Moncrieff AE, Leite RN, Brumfield RT, Braun EL, Kimball RT. Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae). Syst Biol 2023; 72:161-178. [PMID: 36130303 PMCID: PMC10452962 DOI: 10.1093/sysbio/syac062] [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: 10/20/2021] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation].
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Affiliation(s)
- Min Zhao
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Sarah M Kurtis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Noor D White
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, Bethesda, MD 20892, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Andre E Moncrieff
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USAand
| | - Rafael N Leite
- Graduate Program in Ecology, National Institute of Amazonian Research, Manaus, AM, Brazil
| | - Robb T Brumfield
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USAand
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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26
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Benítez-Villaseñor A, Granados Mendoza C, Wanke S, Peñafiel Cevallos M, Freire ME, Lemmon EM, Lemmon AR, Magallón S. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 2023; 181:107714. [PMID: 36708940 DOI: 10.1016/j.ympev.2023.107714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Anchored Hybrid Enrichment (AHE) is a tool for capturing orthologous regions of the nuclear genome shared in low or single copy across lineages. Despite the increasing number of studies using this method, its usefulness to estimate relationships at deeper taxonomic levels in plants has not been fully explored. Here we present a proof of concept about the performance of nuclear loci obtained with AHE to infer phylogenetic relationships and explore the use of gene sampling schemes to estimate divergence times in Asterales. We recovered low-copy nuclear loci using the AHE method from herbarium material and silica-preserved samples. Maximum likelihood, Bayesian inference, and coalescence approaches were used to reconstruct phylogenomic relationships. Dating analyses were conducted under a multispecies coalescent approach by jointly inferring species tree and divergence times with random gene sampling schemes and multiple calibrations. We recovered 403 low-copy nuclear loci for 63 species representing nine out of eleven families of Asterales. Phylogenetic hypotheses were congruent among the applied methods and previously published results. Analyses with concatenated datasets were strongly supported, but coalescence-based analyses showed low support for the phylogenetic position of families Argophyllaceae and Alseuosmiaceae. Estimated family ages were congruent among gene sampling schemes, with the mean age for Asterales around 130 Myr. Our study documents the usefulness of AHE for resolving phylogenetic relationships at deep phylogenetic levels in Asterales. Observed phylogenetic inconsistencies were possibly due to the non-inclusion of families Phellinceae and Pentaphragmataceae. Random gene sampling schemes produced consistent age estimates with coalescence and species tree relaxed clock approaches.
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Affiliation(s)
- Adriana Benítez-Villaseñor
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, C.P.04510 Ciudad de México, Mexico.
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Marcia Peñafiel Cevallos
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - M Efraín Freire
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, United States.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306-4120, United States.
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico.
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27
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Mulhair PO, McCarthy CGP, Siu-Ting K, Creevey CJ, O'Connell MJ. Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life. Curr Biol 2022; 32:5180-5188.e3. [PMID: 36356574 DOI: 10.1016/j.cub.2022.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/09/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum1,2,3,4,5,6 or within Deuterostomia, sister to Ambulacraria.7,8,9,10,11 Although their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. Recent studies have questioned whether Deuterostomia should be considered monophyletic at all.10,12,13 Hidden paralogy and poor phylogenetic signal present a major challenge for reconstructing species phylogenies.14,15,16,17,18 Here, we assess whether these issues have contributed to the conflict over the placement of Xenacoelomorpha. We reanalyzed published datasets, enriching for orthogroups whose gene trees support well-resolved clans elsewhere in the animal tree.16 We find that most genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy and low phylogenetic signal affect the ability to reconstruct branching patterns at deep nodes in the animal tree. We demonstrate that removing orthogroups that cannot recapitulate incontestable relationships alters the final topology that is inferred, while simultaneously improving the fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our set of filtered orthogroups. At a time when we are progressing toward sequencing all life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modeled adequately.19.
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Affiliation(s)
- Peter O Mulhair
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Charley G P McCarthy
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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Lozano-Fernandez J. A Practical Guide to Design and Assess a Phylogenomic Study. Genome Biol Evol 2022; 14:evac129. [PMID: 35946263 PMCID: PMC9452790 DOI: 10.1093/gbe/evac129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
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Affiliation(s)
- Jesus Lozano-Fernandez
- Department of Genetics, Microbiology and Statistics, Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal 643, 08028 Barcelona, Spain
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra), Passeig marítim de la Barcelona 37-49, 08003 Barcelona, Spain
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29
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Smith BT, Merwin J, Provost KL, Thom G, Brumfield RT, Ferreira M, Mauck Iii WM, Moyle RG, Wright T, Joseph L. Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance. Syst Biol 2022; 72:228-241. [PMID: 35916751 DOI: 10.1093/sysbio/syac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/22/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Jon Merwin
- Department of Ornithology, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA.,Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, PA 19103, USA
| | - Kaiya L Provost
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, RR, Brazil
| | - William M Mauck Iii
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA
| | - Timothy Wright
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
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30
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Uribe JE, González VL, Irisarri I, Kano Y, Herbert DG, Strong EE, Harasewych MG. A phylogenomic backbone for gastropod molluscs. Syst Biol 2022; 71:1271-1280. [PMID: 35766870 DOI: 10.1093/sysbio/syac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Gastropods have survived several mass extinctions during their evolutionary history resulting in extraordinary diversity in morphology, ecology, and developmental modes, which complicate the reconstruction of a robust phylogeny. Currently, gastropods are divided into six subclasses: Caenogastropoda, Heterobranchia, Neomphaliones, Neritimorpha, Patellogastropoda, and Vetigastropoda. Phylogenetic relationships among these taxa historically lack consensus, despite numerous efforts using morphological and molecular information. We generated sequence data for transcriptomes derived from twelve taxa belonging to clades with little or no prior representation in previous studies in order to infer the deeper cladogenetic events within Gastropoda and, for the first time, infer the position of the deep-sea Neomphaliones using a phylogenomic approach. We explored the impact of missing data, homoplasy, and compositional heterogeneity on the inferred phylogenetic hypotheses. We recovered a highly supported backbone for gastropod relationships that is congruent with morphological and mitogenomic evidence, in which Patellogastropoda, true limpets, are the sister lineage to all other gastropods (Orthogastropoda) which are divided into two main clades (i) Vetigastropoda s.l. (including Pleurotomariida + Neomphaliones) and (ii) Neritimorpha + (Caenogastropoda + Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia.
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Affiliation(s)
- Juan E Uribe
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
| | - Vanessa L González
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, and Campus Institute Data Science (CIDAS), Göttingen, Germany.,Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Yasunori Kano
- Department of Marine Ecosystems Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - David G Herbert
- Department of Natural Sciences, National Museum Wales, Cathays Park, Cardiff, CF10 3NP, UK
| | - Ellen E Strong
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
| | - M G Harasewych
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
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31
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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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32
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Owen CL, Marshall DC, Wade EJ, Meister R, Goemans G, Kunte K, Moulds M, Hill K, Villet M, Pham TH, Kortyna M, Lemmon EM, Lemmon AR, Simon C. Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta: Hemiptera). Syst Biol 2022; 71:1504-1523. [PMID: 35708660 DOI: 10.1093/sysbio/syac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a dataset generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the AHE markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned dataset, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution.
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Affiliation(s)
- Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - David C Marshall
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Elizabeth J Wade
- Dept. of Natural Science and Mathematics, Curry College, Milton, MA 02186, USA
| | - Russ Meister
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Geert Goemans
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Max Moulds
- Australian Museum Research Institute, 1 William Street, Sydney N.S.W, Australia. 2010
| | - Kathy Hill
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - M Villet
- Dept. of Biology, Rhodes University, Grahamstown 6140, South Africa
| | - Thai-Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hue, Vietnam.,Vietnam National Museum of Nature and Graduate School of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Michelle Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Chris Simon
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
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33
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Lagomarsino LP, Frankel L, Uribe-Convers S, Antonelli A, Muchhala N. Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation. ANNALS OF BOTANY 2022; 129:723-736. [PMID: 35363863 PMCID: PMC9113290 DOI: 10.1093/aob/mcac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/24/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centred rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. METHODS Targeted sequence capture using a probe-set recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. KEY RESULTS While silica-dried leaf tissue resulted in longer assembled sequence data, the inclusion of herbarium samples improved taxonomic representation. Relationships among baccate lineages are similar to those inferred in previous studies, although they differ for lineages within and among capsular clades. We improve the phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. CONCLUSIONS This first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict and well-supported differences between analyses based on different nuclear loci. Together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is probably present in many other species-rich Andean plant radiations.
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Affiliation(s)
- Laura P Lagomarsino
- Shirley C. Tucker Herbarium, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Lauren Frankel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Simon Uribe-Convers
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
- Invitae Corporation, San Francisco, CA, USA
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Science, University of Oxford, Oxford, UK
| | - Nathan Muchhala
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
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34
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Steenwyk JL, Buida Iii TJ, Gonçalves C, Goltz DC, Morales G, Mead ME, LaBella AL, Chavez CM, Schmitz JE, Hadjifrangiskou M, Li Y, Rokas A. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics 2022; 221:6583183. [PMID: 35536198 PMCID: PMC9252278 DOI: 10.1093/genetics/iyac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022] Open
Abstract
Bioinformatic analysis-such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, file format conversion, and processing and analysis-is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses, but unified toolkits that conduct all these analyses are lacking. To address this gap, we introduce BioKIT, a versatile command line toolkit that has, upon publication, 42 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we conducted a comprehensive examination of relative synonymous codon usage across 171 fungal genomes that use alternative genetic codes, showed that the novel metric of gene-wise relative synonymous codon usage can accurately estimate gene-wise codon optimization, evaluated the quality and characteristics of 901 eukaryotic genome assemblies, and calculated alignment summary statistics for 10 phylogenomic data matrices. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwyk-biokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).
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Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.,Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | | | - Grace Morales
- Department of Pathology, Microbiology & Immunology, Center for Personalized Microbiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew E Mead
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Christina M Chavez
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan E Schmitz
- Department of Pathology, Microbiology & Immunology, Center for Personalized Microbiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maria Hadjifrangiskou
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.,Department of Pathology, Microbiology & Immunology, Center for Personalized Microbiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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Krug PJ, Caplins SA, Algoso K, Thomas K, Valdés ÁA, Wade R, Wong NLWS, Eernisse DJ, Kocot KM. Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing. Proc Biol Sci 2022; 289:20211855. [PMID: 35382597 PMCID: PMC8984808 DOI: 10.1098/rspb.2021.1855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/21/2022] [Indexed: 11/12/2022] Open
Abstract
Transitions to terrestriality have been associated with major animal radiations including land snails and slugs in Stylommatophora (>20 000 described species), the most successful lineage of 'pulmonates' (a non-monophyletic assemblage of air-breathing gastropods). However, phylogenomic studies have failed to robustly resolve relationships among traditional pulmonates and affiliated marine lineages that comprise clade Panpulmonata (Mollusca, Gastropoda), especially two key taxa: Sacoglossa, a group including photosynthetic sea slugs, and Siphonarioidea, intertidal limpet-like snails with a non-contractile pneumostome (narrow opening to a vascularized pallial cavity). To clarify the evolutionary history of the panpulmonate radiation, we performed phylogenomic analyses on datasets of up to 1160 nuclear protein-coding genes for 110 gastropods, including 40 new transcriptomes for Sacoglossa and Siphonarioidea. All 18 analyses recovered Sacoglossa as the sister group to a clade we named Pneumopulmonata, within which Siphonarioidea was sister to the remaining lineages in most analyses. Comparative modelling indicated shifts to marginal habitat (estuarine, mangrove and intertidal zones) preceded and accelerated the evolution of a pneumostome, present in the pneumopulmonate ancestor along with a one-sided plicate gill. These findings highlight key intermediate stages in the evolution of air-breathing snails, supporting the hypothesis that adaptation to marginal zones played an important role in major sea-to-land transitions.
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Affiliation(s)
- Patrick J. Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | | | - Krisha Algoso
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Kanique Thomas
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA
| | - Ángel A. Valdés
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Rachael Wade
- Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nur Leena W. S. Wong
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Douglas J. Eernisse
- Department of Biological Science, California State University, Fullerton, CA 92834, USA
| | - Kevin M. Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, AL 35487, USA
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36
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Mongiardino Koch N, Thompson JR, Hiley AS, McCowin MF, Armstrong AF, Coppard SE, Aguilera F, Bronstein O, Kroh A, Mooi R, Rouse GW. Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. eLife 2022; 11:72460. [PMID: 35315317 PMCID: PMC8940180 DOI: 10.7554/elife.72460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Earth & Planetary Sciences, Yale University, New Haven, United States.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Jeffrey R Thompson
- Department of Earth Sciences, Natural History Museum, London, United Kingdom.,University College London Center for Life's Origins and Evolution, London, United Kingdom
| | - Avery S Hiley
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Marina F McCowin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - A Frances Armstrong
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Simon E Coppard
- Bader International Study Centre, Queen's University, Herstmonceux Castle, East Sussex, United Kingdom
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, Vienna, Austria
| | - Rich Mooi
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
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37
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Ballesteros JA, Santibáñez-López CE, Baker CM, Benavides LR, Cunha TJ, Gainett G, Ontano AZ, Setton EVW, Arango CP, Gavish-Regev E, Harvey MS, Wheeler WC, Hormiga G, Giribet G, Sharma PP. Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida. Mol Biol Evol 2022; 39:6522129. [PMID: 35137183 PMCID: PMC8845124 DOI: 10.1093/molbev/msac021] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Carlos E Santibáñez-López
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biology, Western Connecticut State University, Danbury, CT, 06810, USA
| | - Caitlin M Baker
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Ligia R Benavides
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Tauana J Cunha
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Andrew Z Ontano
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Claudia P Arango
- Office for Research, Griffith University, Nathan, Queensland, 4111, Australia
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Mark S Harvey
- Collections & Research, Western Australian Museum, Welshpool, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western, Crawley, Western Australia, 6009, Australia; Australia
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Superson A, Battistuzzi F. Exclusion of fast evolving genes or fast evolving sites produces different archaean phylogenies. Mol Phylogenet Evol 2022; 170:107438. [DOI: 10.1016/j.ympev.2022.107438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 01/07/2022] [Accepted: 02/03/2022] [Indexed: 11/26/2022]
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Carruthers T, Sun M, Baker WJ, Smith SA, de Vos JM, Eiserhardt WL. OUP accepted manuscript. Syst Biol 2022; 71:1124-1146. [PMID: 35167690 PMCID: PMC9366463 DOI: 10.1093/sysbio/syac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from the erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analyzing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with the species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation. [Divergence time estimation; gene trees; species tree; topological incongruence.]
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Affiliation(s)
- Tom Carruthers
- Correspondence to be sent to: Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; E-mail:
| | - Miao Sun
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Jurriaan M de Vos
- Department of Environmental Sciences – Botany, University of Basel, 4056 Basel, Switzerland
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
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Ontano AZ, Steiner HG, Sharma PP. How many long branch orders occur in Chelicerata? Opposing effects of Palpigradi and Opilioacariformes on phylogenetic stability. Mol Phylogenet Evol 2021; 168:107378. [PMID: 34968680 DOI: 10.1016/j.ympev.2021.107378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 01/20/2023]
Abstract
Excepting a handful of nodes, phylogenetic relationships between chelicerate orders remains poorly resolved, due to both the incidence of long branch attraction artifacts and the limited sampling of key lineages. It has recently been shown that increasing representation of basal nodes plays an outsized role in resolving the higher-level placement of long branch chelicerate orders. Two lineages have been consistently undersampled in chelicerate phylogeny. First, sampling of the miniaturized order Palpigradi has been restricted to a fragmentary transcriptome of a single species. Second, sampling of Opilioacariformes, a rarely encountered and key group of Parasitiformes, has been restricted to a single exemplar. These two lineages exhibit dissimilar properties with respect to branch length; Opilioacariformes shows relatively low evolutionary rate compared to other Parasitiformes, whereas Palpigradi possibly acts as another long branch order (an effect that may be conflated with the degree of missing data). To assess these properties and their effects on tree stability, we constructed a phylogenomic dataset of Chelicerata wherein both lineages were sampled with three terminals, increasing the representation of these lineages per locus. We examined the effect of subsampling phylogenomic matrices using (1) taxon occupancy, (2) evolutionary rate, and (3) a principal components-based approach. We further explored the impact of taxon deletion experiments that mitigate the effect of long branches. Here, we show that Palpigradi constitutes a fourth long branch chelicerate order (together with Acariformes, Parasitiformes, and Pseudoscorpiones), which further destabilizes the chelicerate backbone topology. By contrast, the slow-evolving Opilioacariformes were consistently recovered within Parasitiformes, with certain subsampling practices recovering their placement as the sister group to the remaining Parasitiformes. Whereas the inclusion of Opilioacariformes always resulted in the non-monophyly of Acari with support, deletion of Opilioacariformes from datasets consistently incurred the monophyly of Acari except in matrices constructed on the basis of evolutionary rate. Our results strongly suggest that Acari is an artifact of long-branch attraction.
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Affiliation(s)
- Andrew Z Ontano
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA 53706
| | - Hugh G Steiner
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA 53706
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA 53706.
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What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata. DIVERSITY 2021. [DOI: 10.3390/d13110568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.
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Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D. The evolution of insect biodiversity. Curr Biol 2021; 31:R1299-R1311. [PMID: 34637741 DOI: 10.1016/j.cub.2021.08.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.
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Affiliation(s)
- Erik Tihelka
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Chenyang Cai
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | | | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, Bristol, UK; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige, Italy; Center Agriculture Food Environment, University of Trento, 38010 San Michele all Adige, Italy
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, KS, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK.
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Lee AK, Gilman IS, Srivastav M, Lerner AD, Donoghue MJ, Clement WL. Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights. AMERICAN JOURNAL OF BOTANY 2021; 108:1122-1142. [PMID: 34254290 PMCID: PMC8362060 DOI: 10.1002/ajb2.1695] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/12/2021] [Indexed: 05/04/2023]
Abstract
PREMISE Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times. METHODS Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off-target reads, and 10 fossils were used to calibrate dated trees. RESULTS Varying numbers of targeted loci and off-target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm-wide dating analyses, but many major splitting events date to the Eocene. CONCLUSIONS The Angiosperms353 probe set facilitated the assembly of a large, single-copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.
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Affiliation(s)
- Aaron K. Lee
- Department of BiologyThe College of New JerseyEwingNJ08628USA
- Department of Plant and Microbial BiologyUniversity of Minnesota ‐ Twin CitiesSaint PaulMN55108USA
| | - Ian S. Gilman
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Mansa Srivastav
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Ariel D. Lerner
- Department of BiologyThe College of New JerseyEwingNJ08628USA
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
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