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Chang SC, Ahyong ST, Tsang LM. Molecular phylogeny of deep-sea blind lobsters of the family Polychelidae (Decapoda: Polychelida), with implications for the origin and evolution of these "living fossils". Mol Phylogenet Evol 2024; 192:107998. [PMID: 38142793 DOI: 10.1016/j.ympev.2023.107998] [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: 08/10/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
A comprehensive molecular analysis of the deep-sea blind lobsters of the family Polychelidae, often referred to as "living fossils", is conducted based on all six modern genera and 27 of the 38 extant species. Using six genetic markers from both mitochondrial and nuclear genomes, the molecular phylogenetic results differ considerably from previous morphological analyses and reveal the genera Polycheles and Pentacheles to be para- or polyphyletic. As the splitting of Polycheles has strong support from both molecular and morphological data, two new genera, Dianecheles and Neopolycheles, are erected for those species excluded from the clade containing the type species of Polycheles. The pattern of polyphyly of Pentacheles, however, is not robustly resolved, so it is retained as a single genus. Fossil evidence suggests that fossil polychelids inhabited deep-sea environments as early as the Early to Middle Jurassic, demonstrating the enduring adaptation of extant polychelid species to the deep-sea. Time-calibrated phylogeny suggested that modern polychelids probably had an Atlantic origin during the Jurassic period. Since their emergence, this ancient lobster group has continued to diversify, particularly in the West Pacific, and has colonized the abyssal zone, with the deepest genus, Willemoesia, representing the more 'derived' members among extant polychelids. Differences in eye reduction among extant polychelid genera highlight the necessity for ongoing investigations to ascertain the relative degree of functionality of their eyes, if they indeed retain any function.
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Affiliation(s)
- Su-Ching Chang
- Department of Biological Resources, National Chiayi University, Chiayi 600355, Taiwan, ROC
| | - Shane T Ahyong
- Australian Museum, 1 William St, Sydney, NSW 2010, Australia; School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Ling-Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Ruan X, Cheng H, Xuan Z, Li Z, Yu J, Zhao H. The complete mitochondrial genome of Allogalathea elegans (Adams & White, 1848) (Decapoda: Galatheidae). Mitochondrial DNA B Resour 2023; 8:857-861. [PMID: 37583939 PMCID: PMC10424596 DOI: 10.1080/23802359.2023.2242625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
The genus Allogalathea belongs to the subfamily Galatheoidea of the family Galatheidae. Here, we report a mitogenome of Allogalathea elegans (Adams & White, 1848). In this study, we obtained the complete mitochondrial genome of Allogalathea elegans by sequencing, which was 16,263 bp in length. The mitogenome contained 37 genes, including the typical set of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 Ribosomal RNA (rRNA) genes. The nucleotides A, C, G, and T distribution was 36.40%, 19.44%, 9.09%, and 35.07%, respectively. The length of the total protein-coding genes was 11,172 bp, which accounts for 68.69% of the whole mitochondrial genome. The phylogenetic result generated by IQ-Tree based on 13 PGCs showed that the infraorder Anomura is monophyletic, and the infraorder Anomura is a sister group of the infraorder Glypheidea. The discovery of the complete mitochondrial genome of A. elegans would help to conduct in-depth research on the infraorder Anomura.
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Affiliation(s)
- Xinhe Ruan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Huitao Cheng
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zijie Xuan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zongyang Li
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jie Yu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Huihong Zhao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
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Wolfe JM, Luque J, Bracken-Grissom HD. How to become a crab: Phenotypic constraints on a recurring body plan. Bioessays 2021; 43:e2100020. [PMID: 33751651 DOI: 10.1002/bies.202100020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab-like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as "carcinization." The repeated loss of this body plan has been identified as "decarcinization." In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab-like body form.
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Affiliation(s)
- Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Javier Luque
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Smithsonian Tropical Research Institute, Balboa-Ancon, Panama.,Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
| | - Heather D Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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Scholtz G. Eocarcinus praecursor Withers, 1932 (Malacostraca, Decapoda, Meiura) is a stem group brachyuran. ARTHROPOD STRUCTURE & DEVELOPMENT 2020; 59:100991. [PMID: 32891896 DOI: 10.1016/j.asd.2020.100991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Beginning with the description by Withers in 1932, Eocarcinus praecursor from the Jurassic has long been considered the oldest representative of the Brachyura. In 2010 Feldmann and Schweitzer re-investigated the specimens of E. praecursor and expressed doubts about the brachyuran nature of this species. Among other characters, the suspected existence of small chelae in the 2nd or 3rd pereopods led them to the conclusion that E. praecursor must be removed from the Brachyura and rather be seen as a representative of the Anomala. However, Anomala also do not possess chelae on the 2nd and 3rd pereopods. This contradiction and other aspects initiated a new investigation of E. praecursor. It can be shown that neither the 2nd nor the 3rd pereopods of E. praecursor are chelate. Furthermore, there are no other derived characters shared with anomalans. By contrast, there are a number of apomorphies shared with Brachyura such as the shape and articulation of the large chelae and the attachment points of the last two pereopods. However, not all apomorphies of the crown group are present yet. Thus, E. praecursor is a stem group representative, which allows statements about individual steps in the evolution of the set of characters of the crown group Brachyura.
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Affiliation(s)
- Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie/Vergleichende Zoologie, Philippstr. 13, 10115 Berlin, Germany.
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Wolfe JM, Breinholt JW, Crandall KA, Lemmon AR, Lemmon EM, Timm LE, Siddall ME, Bracken-Grissom HD. A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans. Proc Biol Sci 2020; 286:20190079. [PMID: 31014217 DOI: 10.1098/rspb.2019.0079] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
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Affiliation(s)
- Joanna M Wolfe
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA.,2 Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology , Cambridge, MA 02139 , USA.,3 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
| | - Jesse W Breinholt
- 4 Florida Museum of Natural History, University of Florida , Gainesville, FL 32611 , USA.,5 RAPiD Genomics , Gainesville, FL 32601 , USA
| | - Keith A Crandall
- 6 Computational Biology Institute, The George Washington University , Ashburn, VA 20147 , USA.,7 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC 20012 , USA
| | - Alan R Lemmon
- 8 Department of Scientific Computing, Florida State University , Dirac Science Library, Tallahassee, FL 32306 , USA
| | - Emily Moriarty Lemmon
- 9 Department of Biological Science, Florida State University , Tallahassee, FL 32306 , USA
| | - Laura E Timm
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
| | - Mark E Siddall
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA
| | - Heather D Bracken-Grissom
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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Gan HM, Linton SM, Austin CM. Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes. Mar Genomics 2019; 45:64-71. [DOI: 10.1016/j.margen.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 01/01/2023]
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Gan HM, Grandjean F, Jenkins TL, Austin CM. Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication. BMC Genomics 2019; 20:335. [PMID: 31053062 PMCID: PMC6500004 DOI: 10.1186/s12864-019-5704-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 04/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation. RESULTS We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes. CONCLUSIONS Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220 Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220 Australia
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Malaysia
- Monash University Malaysia Genomics Facility, Monash University, Bandar Sunway, 47500 Petaling Jaya, Malaysia
| | - Frederic Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose 5 rue Albert Turpin, 86073 Poitiers, Cedex, France
| | - Tom L. Jenkins
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Christopher Mervyn Austin
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220 Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220 Australia
- School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Malaysia
- Monash University Malaysia Genomics Facility, Monash University, Bandar Sunway, 47500 Petaling Jaya, Malaysia
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ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Mol Phylogenet Evol 2018; 127:320-331. [DOI: 10.1016/j.ympev.2018.05.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/03/2018] [Accepted: 05/13/2018] [Indexed: 01/08/2023]
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