1
|
Treleven CR, Kishe MA, Silas MO, Ngatunga BP, Kuboja BN, Mgeleka SS, Taylor AL, Elsmore MAM, Healey AJE, Sauer WHH, Shaw PW, McKeown NJ. Genetic analysis of Octopus cyanea reveals high gene flow in the South-West Indian Ocean. Ecol Evol 2024; 14:e11205. [PMID: 38584773 PMCID: PMC10994983 DOI: 10.1002/ece3.11205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Octopus cyanea (Gray, 1849), abundant in the South-West Indian Ocean (SWIO), constitutes a vital resource for both subsistence and commercial fisheries. However, despite this socioeconomic importance, and recent indications of overfishing, little is known about the population structure of O. cyanea in the region. To inform sustainable management strategies, this study assessed the spatio-temporal population structure and genetic variability of O. cyanea at 20 sites in the SWIO (Kenya, Tanzania, Mozambique, Madagascar, Mauritius, Rodrigues, and the Seychelle Islands) by complementary analysis of mitochondrial DNA (mtDNA) noncoding region (NCR) sequences and microsatellite markers. MtDNA analysis revealed a shallow phylogeny across the region, with demographic tests suggesting historic population fluctuations that could be linked to glacial cycles. Contrary to expectations, NCR variation was comparable to other mtDNA regions, indicating that the NCR is not a hypervariable region. Both nuclear and mtDNA marker types revealed a lack of genetic structure compatible with high gene flow throughout the region. As adults are sedentary, this gene flow likely reflects connectivity by paralarval dispersal. All samples reported heterozygote deficits, which, given the overall absence of structure, likely reflect ephemeral larval recruitment variability. Levels of mtDNA and nuclear variability were similar at all locations and congruent with those previously reported for harvested Octopodidae, implying resilience to genetic erosion by drift, providing current stock sizes are maintained. However, as O. cyanea stocks in the SWIO represent a single, highly connected population, fisheries may benefit from additional management measures, such as rotational closures aligned with paralarval ecology and spanning geopolitical boundaries.
Collapse
Affiliation(s)
| | - Mary A. Kishe
- Fisheries Research Institute (TAFIRI)Dar es SalaamTanzania
| | | | | | | | - Said S. Mgeleka
- Fisheries Research Institute (TAFIRI)Dar es SalaamTanzania
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Amy L. Taylor
- Department of Life SciencesAberystwyth UniversityAberystwythUK
| | | | | | - Warwick H. H. Sauer
- Department of Ichthyology & Fisheries ScienceRhodes UniversityMakhandaSouth Africa
| | - Paul W. Shaw
- Department of Life SciencesAberystwyth UniversityAberystwythUK
| | | |
Collapse
|
2
|
Lan G, Yu J, Liu J, Zhang Y, Ma R, Zhou Y, Zhu B, Wei W, Liu J, Qi G. Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae). Genes (Basel) 2024; 15:90. [PMID: 38254979 PMCID: PMC10815732 DOI: 10.3390/genes15010090] [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: 11/09/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.
Collapse
Affiliation(s)
- Guanwei Lan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Jiaojiao Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Juan Liu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Yue Zhang
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Rui Ma
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Yanshan Zhou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Biqing Zhu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
| | - Jiabin Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guilan Qi
- Animal Husbandry Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| |
Collapse
|
3
|
Fernández-Álvarez FÁ, Sanchez G, Deville D, Taite M, Villanueva R, Allcock AL. Atlantic Oceanic Squids in the "Grey Speciation Zone". Integr Comp Biol 2023; 63:1214-1225. [PMID: 37604791 PMCID: PMC10755182 DOI: 10.1093/icb/icad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/03/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023] Open
Abstract
Cryptic species complexes represent an important challenge for the adequate characterization of Earth's biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the "grey speciation zone." As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.
Collapse
Affiliation(s)
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0412, Japan
| | - Diego Deville
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima 739-8528, Japan
| | - Morag Taite
- Ryan Institute and School of Natural Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
| | - Roger Villanueva
- Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim de la Barceloneta 37–49, 08003 Barcelona, Spain
| | - A Louise Allcock
- Ryan Institute and School of Natural Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
| |
Collapse
|
4
|
Jeena NS, Sajikumar KK, Rahuman S, Ragesh N, Koya KPS, Chinnadurai S, Sasikumar G, Mohamed KS. Insights into the divergent evolution of the oceanic squid Sthenoteuthis oualaniensis (Cephalopoda: Ommastrephidae) from the Indian Ocean. Integr Zool 2023; 18:924-948. [PMID: 36610009 DOI: 10.1111/1749-4877.12705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms (viz. middle-sized, dwarf, and giant forms) whose taxonomic status has been disputed for decades. This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species. Molecular analyses employing mitochondrial (COI, ND2) and nuclear (H3) markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean, representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean. The mitochondrial-based phylograms revealed two distinct clades in the species: "dwarf forms + giant form" and "middle-sized forms," which further branch into geographically structured evolutionary units. Species delimitation analyses recovered five distinct clades, namely, the Arabian Sea giant and dwarf forms, Equatorial, Eastern Typical, and Other Middle-sized forms, representing the consensus molecular operational taxonomic units. H3 being heterozygous could not resolve the phylogeny. Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes, whereas these outputs and PCA results were incongruent with the morphological grouping. Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes. The giant form was genetically close to the dwarf forms, contradicting the earlier notion that it descended from the middle-sized form. It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters, while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.
Collapse
Affiliation(s)
- Nikarthil S Jeena
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | | | - Summaya Rahuman
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Nadakkal Ragesh
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - K P Said Koya
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Shunmugavel Chinnadurai
- Fishing Technology Division, Veraval Research Centre of ICAR-Central Institute of Fisheries Technology, Matsyabhavan, Bhidia, Veraval, Gujarat, India
| | - Geetha Sasikumar
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | | |
Collapse
|
5
|
Ifrim C, Stinnesbeck W, González González AH, Schorndorf N, Gale AS. Ontogeny, evolution and palaeogeographic distribution of the world's largest ammonite Parapuzosia (P.) seppenradensis (Landois, 1895). PLoS One 2021; 16:e0258510. [PMID: 34758037 PMCID: PMC8580234 DOI: 10.1371/journal.pone.0258510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
The world’s largest ammonite, Parapuzosia (P.) seppenradensis (Landois, 1895), fascinated the world ever since the discovery, in 1895, of a specimen of 1.74 metres (m) diameter near Seppenrade in Westfalia, Germany, but subsequent findings of the taxon are exceedingly rare and its systematic position remains enigmatic. Here we revise the historical specimens and document abundant new material from England and Mexico. Our study comprises 154 specimens of large (< 1 m diameter) to giant (> 1m diameter) Parapuzosia from the Santonian and lower Campanian, mostly with stratigraphic information. High-resolution integrated stratigraphy allows for precise cross-Atlantic correlation of the occurrences. Our specimens were analysed regarding morphometry, growth stages and stratigraphic occurrence wherever possible. Our analysis provides insight into the ontogeny of Parapuzosia (P.) seppenradensis and into the evolution of this species from its potential ancestor P. (P.) leptophylla Sharpe, 1857. The latter grew to shell diameters of about 1 m and was restricted to Europe in the early Santonian, but it reached the Gulf of Mexico during the late Santonian. P. (P.) seppenradensis first appears in the uppermost Santonian- earliest Campanian on both sides of the Atlantic. Initially, it also reached diameters of about 1 m, but gradual evolutionary increase in size is seen in the middle early Campanian to diameters of 1.5 to 1.8 m. P. (P.) seppenradensis is characterized by five ontogenetic growth stages and by size dimorphism. We therefore here include the many historic species names used in the past to describe the morphological and size variability of the taxon. The concentration of adult shells in small geographic areas and scarcity of Parapuzosia in nearby coeval outcrop regions may point to a monocyclic, possibly even semelparous reproduction strategy in this giant cephalopod. Its gigantism exceeds a general trend of size increase in late Cretaceous cephalopods. Whether the coeval increase in size of mosasaurs, the top predators in Cretaceous seas, caused ecological pressure on Parapuzosia towards larger diameters remains unclear.
Collapse
Affiliation(s)
- Christina Ifrim
- Institut für Geowissenschaften, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
- * E-mail:
| | - Wolfgang Stinnesbeck
- Institut für Geowissenschaften, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | | | - Nils Schorndorf
- Institut für Geowissenschaften, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Andrew S. Gale
- School of the Environment, Geography and Geological Sciences, University of Portsmouth, Portsmouth, United Kingdom
- Earth Sciences Department, Natural History Museum, London, United Kingdom
| |
Collapse
|
6
|
Fernández-Álvarez FÁ, Taite M, Vecchione M, Villanueva R, Allcock AL. A phylogenomic look into the systematics of oceanic squids (order Oegopsida). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Abstract
Oceanic squids of the order Oegopsida are ecologically and economically important members of the pelagic environment. They are the most diverse group of cephalopods, with 24 families that are divergent morphologically. Despite their importance, knowledge of phylogenetic relationships among oegopsids is less than that among neritic cephalopods. Here, we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes for 35 selected oceanic squids, which were generated using genome skimming. We performed maximum likelihood and Bayesian inference analyses that included 21 of the 24 oegopsid families. In our analyses, the architeuthid, chiroteuthid and enoploteuthid family groups, which have been proposed previously based on morphological and natural history characteristics, were retrieved as monophyletic. The morphologically divergent Cranchiidae formed a well-supported clade with families Ommastrephidae and Thysanoteuthidae, with a unique mitochondrial gene order. The family Lycoteuthidae was revealed as paraphyletic and contained Pyroteuthidae. Thus, the two lycoteuthid subfamilies are herein elevated to family level, increasing the number of oegopsid squid families to 25. In order to describe the diversity and evolutionary trends of oegopsid squids accurately, the superfamilies Architeuthoidea, Chiroteuthoidea, Cranchioidea and Enoploteuthoidea are resurrected from the literature, and the superfamilies Cycloteuthoidea, Octopoteuthoidea and Pholidoteuthoidea are proposed. The phylogenetic positions of Gonatidae, Histioteuthidae and Onychoteuthidae were not stable in our phylogenetic analyses and are not assigned to a superfamily. This study supports the utility of genome skimming to solve the phylogenetic relationships of oceanic squids.
Collapse
Affiliation(s)
| | - Morag Taite
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, UK
| | - Michael Vecchione
- NOAA/NMFS National Systematics Laboratory, National Museum of Natural History, Washington, DC, USA
| | - Roger Villanueva
- Institut de Ciències del Mar (CSIC), Passeig Marítim 37–49, E-08003 Barcelona, Spain
| | - A Louise Allcock
- Ryan Institute and School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| |
Collapse
|
7
|
Kakui K, Nomaki H, Komatsu H, Fujiwara Y. Unexpected low genetic differentiation between Japan and Bering Sea populations of a deep-sea benthic crustacean lacking a planktonic larval stage (Peracarida: Tanaidacea). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractInformation on the extent, diversity and connectivity of populations is lacking for most deep-sea invertebrates. Species of the order Tanaidacea (Crustacea), one of the most diverse and abundant macrofaunal groups in the deep sea, are benthic, lack a planktonic larval stage, and thus would be expected to have narrow distributional ranges. However, with molecular evidence from the COI gene, we show here that the deep-sea tanaidacean Carpoapseudes spinigena has a distributional range spanning at least 3700 km, from off northern Japan to the south-eastern Bering Sea. Living individuals found in a sediment core indicated that the species is a sedentary burrower. COI analyses revealed a low level of genetic diversity overall, and low differentiation (p-distance, 0.2–0.8%) between the Japan and Bering Sea populations. One hypothesis to explain the low genetic diversity over a broad region is that the Japan population was founded by individuals transported by ocean currents from the Bering Sea. However, due to limited data, other explanations cannot be ruled out. Our results indicate that continued sampling is of fundamental importance to understanding how genetic and taxonomic diversity originate and are maintained in the deep sea.
Collapse
Affiliation(s)
- Keiichi Kakui
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Hidetaka Nomaki
- SUGAR, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hironori Komatsu
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Japan
| | - Yoshihiro Fujiwara
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| |
Collapse
|
8
|
Almeida D, Domínguez-Pérez D, Matos A, Agüero-Chapin G, Osório H, Vasconcelos V, Campos A, Antunes A. Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database. Antibiotics (Basel) 2020; 9:antibiotics9110757. [PMID: 33143020 PMCID: PMC7693380 DOI: 10.3390/antibiotics9110757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022] Open
Abstract
Cephalopods, successful predators, can use a mixture of substances to subdue their prey, becoming interesting sources of bioactive compounds. In addition to neurotoxins and enzymes, the presence of antimicrobial compounds has been reported. Recently, the transcriptome and the whole proteome of the Octopus vulgaris salivary apparatus were released, but the role of some compounds—e.g., histones, antimicrobial peptides (AMPs), and toxins—remains unclear. Herein, we profiled the proteome of the posterior salivary glands (PSGs) of O. vulgaris using two sample preparation protocols combined with a shotgun-proteomics approach. Protein identification was performed against a composite database comprising data from the UniProtKB, all transcriptomes available from the cephalopods’ PSGs, and a comprehensive non-redundant AMPs database. Out of the 10,075 proteins clustered in 1868 protein groups, 90 clusters corresponded to venom protein toxin families. Additionally, we detected putative AMPs clustered with histones previously found as abundant proteins in the saliva of O. vulgaris. Some of these histones, such as H2A and H2B, are involved in systemic inflammatory responses and their antimicrobial effects have been demonstrated. These results not only confirm the production of enzymes and toxins by the O. vulgaris PSGs but also suggest their involvement in the first line of defense against microbes.
Collapse
Affiliation(s)
- Daniela Almeida
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal; (D.A.); (D.D.-P.); (A.M.); (G.A.-C.); (V.V.); (A.C.)
| | - Dany Domínguez-Pérez
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal; (D.A.); (D.D.-P.); (A.M.); (G.A.-C.); (V.V.); (A.C.)
| | - Ana Matos
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal; (D.A.); (D.D.-P.); (A.M.); (G.A.-C.); (V.V.); (A.C.)
- Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Guillermin Agüero-Chapin
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal; (D.A.); (D.D.-P.); (A.M.); (G.A.-C.); (V.V.); (A.C.)
- Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Hugo Osório
- i3S—Instituto de Investigação e Inovação em Saúde-i3S, University of Porto, 4200-135 Porto, Portugal;
- Ipatimup—Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, 4200-135 Porto, Portugal
- Department of Pathology and Oncology of the Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal; (D.A.); (D.D.-P.); (A.M.); (G.A.-C.); (V.V.); (A.C.)
- Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Alexandre Campos
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal; (D.A.); (D.D.-P.); (A.M.); (G.A.-C.); (V.V.); (A.C.)
| | - Agostinho Antunes
- CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal; (D.A.); (D.D.-P.); (A.M.); (G.A.-C.); (V.V.); (A.C.)
- Biology Department of the Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- Correspondence:
| |
Collapse
|
9
|
Quinteiro J, Rodríguez-Castro J, Rey-Méndez M, González-Henríquez N. Phylogeography of the insular populations of common octopus, Octopus vulgaris Cuvier, 1797, in the Atlantic Macaronesia. PLoS One 2020; 15:e0230294. [PMID: 32191765 PMCID: PMC7082011 DOI: 10.1371/journal.pone.0230294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/25/2020] [Indexed: 11/20/2022] Open
Abstract
Exploited, understudied populations of the common octopus, Octopus vulgaris Cuvier, 1797, occur in the northeastern Atlantic (NEA) throughout Macaronesia, comprising the Azores, Madeira and Canaries, and also the Cabo Verde archipelago. This octopus species, found from the intertidal to shallow continental-shelf waters, is largely sedentary, and the subject of intense, frequently unregulated fishing effort. We infer connectivity among insular populations of this octopus. Mitochondrial control region and COX1 sequence datasets reveal two highly divergent haplogroups (α and β) at similar frequencies, with opposing clinal distributions along the sampled latitudinal range. Haplogroups have different demographic and phylogeographic patterns, with origins related to the two last glacial maxima. FST values suggest a significant differentiation for most pairwise comparisons, including insular and continental samples, from the Galicia and Morocco coasts, with the exception of pairwise comparisons for samples from Madeira and the Canaries populations. Results indicate the existence of genetically differentiated octopus populations throughout the NEA. This emphasizes the importance of regulations by autonomous regional governments of the Azores, Madeira and the Canaries, for appropriate management of insular octopus stocks.
Collapse
Affiliation(s)
- Javier Quinteiro
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
- * E-mail:
| | - Jorge Rodríguez-Castro
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
| | - Manuel Rey-Méndez
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
| | - Nieves González-Henríquez
- BIOMOL Laboratory, Department of Biology, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| |
Collapse
|
10
|
Albertin CB, Simakov O. Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties. Annu Rev Anim Biosci 2020; 8:71-90. [PMID: 31815522 DOI: 10.1146/annurev-animal-021419-083609] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond.
Collapse
Affiliation(s)
- Caroline B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA;
| | - Oleg Simakov
- Department of Molecular Evolutionary and Development, University of Vienna, 1090 Vienna, Austria;
| |
Collapse
|
11
|
Sigsgaard EE, Jensen MR, Winkelmann IE, Møller PR, Hansen MM, Thomsen PF. Population-level inferences from environmental DNA-Current status and future perspectives. Evol Appl 2020; 13:245-262. [PMID: 31993074 PMCID: PMC6976968 DOI: 10.1111/eva.12882] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.
Collapse
Affiliation(s)
| | | | | | - Peter Rask Møller
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
| | | | | |
Collapse
|
12
|
da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, Osório H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience 2020; 9:giz152. [PMID: 31942620 PMCID: PMC6962438 DOI: 10.1093/gigascience/giz152] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/27/2019] [Accepted: 12/05/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. FINDINGS We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. CONCLUSIONS This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
Collapse
Affiliation(s)
- Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Alvarina Couto
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| | - Andre M Machado
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
| | - Brona Brejova
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovak Republic
| | - Carolin B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Filipe Silva
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Paul Gardner
- Department of Biochemistry, University of Otago, 710 Cumberland Street, North Dunedin, Dunedin 9016, New Zealand
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Alexandre Campos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
| | - Ângela M Ribeiro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
| | - Inigo Barrio-Hernandez
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Henk-Jan Hoving
- GEOMAR Helmholtz Centre for Ocean Research Kiel,Wischhofstraße 1-3, 24148 Kiel, Germany
| | - Ricardo Tafur-Jimenez
- Instituto del Mar del Perú, Esq. Gamarra y Gral. Valle, Chucuito Apartado 22, Callao, Peru
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Barbara Frazão
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- IPMA, Fitoplâncton Lab, Rua C do Aeroporto, 1749-077, Lisboa, Portugal
| | - Bent Petersen
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Batu 3 1/2, Butik Air Nasi, 08100 Bedong, Kedah, Malaysia
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen,Øster Farimagsgade 5, 1353 Copenhagen, Denmark
| | - Fernando Peñaloza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México
| | - Francesco Musacchia
- Genomic Medicine, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy
| | - Graham C Alexander
- GCB Sequencing and Genomic Technologies Shared Resource, Duke University CIEMAS, 101 Science Drive, Durham, NC 27708, USA
| | - Hugo Osório
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal
| | - Inger Winkelmann
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14 (UZA1), A-1090 Vienna, Austria
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - M Ziaur Rahman
- Bioinformatics Solutions Inc, 470 Weber St N Suite 204, Waterloo, ON N2L 6J2, Canada
| | - Davide Pisani
- School of Biological Sciences and School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TG, UK
| | - Jakob Vinther
- School of Biological Sciences and School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TG, UK
| | - Erich Jarvis
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries & Aquaculture, James Cook University, Townsville, Douglas QLD 4814, Australia
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne Victoria 3086, Australia
| | - L Filipe C Castro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Olivier Fedrigo
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Qiye Li
- BGI-Shenzhen, Shenzhen, China
| | - Sara Rocha
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
- Biomedical Research Center (CINBIO), University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Agostinho Antunes
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Yufeng Wu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Bin Ma
- School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Tomas Vinar
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovak Republic
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Batu 3 1/2, Butik Air Nasi, 08100 Bedong, Kedah, Malaysia
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen,Øster Farimagsgade 5, 1353 Copenhagen, Denmark
| | - Rasmus Nielsen
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Departments of Integrative Biology and Statistics, University of California, 3040 Valley Life Sciences, Berkeley, CA 94720-3200, USA
| | - M Thomas P Gilbert
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Høgskolering 1, 7491 Trondheim, Norway
| |
Collapse
|
13
|
Ritschard EA, Whitelaw B, Albertin CB, Cooke IR, Strugnell JM, Simakov O. Coupled Genomic Evolutionary Histories as Signatures of Organismal Innovations in Cephalopods: Co-evolutionary Signatures Across Levels of Genome Organization May Shed Light on Functional Linkage and Origin of Cephalopod Novelties. Bioessays 2019; 41:e1900073. [PMID: 31664724 DOI: 10.1002/bies.201900073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/05/2019] [Indexed: 12/07/2023]
Abstract
How genomic innovation translates into organismal organization remains largely unanswered. Possessing the largest invertebrate nervous system, in conjunction with many species-specific organs, coleoid cephalopods (octopuses, squids, cuttlefishes) provide exciting model systems to investigate how organismal novelties evolve. However, dissecting these processes requires novel approaches that enable deeper interrogation of genome evolution. Here, the existence of specific sets of genomic co-evolutionary signatures between expanded gene families, genome reorganization, and novel genes is posited. It is reasoned that their co-evolution has contributed to the complex organization of cephalopod nervous systems and the emergence of ecologically unique organs. In the course of reviewing this field, how the first cephalopod genomic studies have begun to shed light on the molecular underpinnings of morphological novelty is illustrated and their impact on directing future research is described. It is argued that the application and evolutionary profiling of evolutionary signatures from these studies will help identify and dissect the organismal principles of cephalopod innovations. By providing specific examples, the implications of this approach both within and beyond cephalopod biology are discussed.
Collapse
Affiliation(s)
- Elena A Ritschard
- Department for Molecular Evolution and Development, University of Vienna, Austria
| | - Brooke Whitelaw
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | | | - Ira R Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Oleg Simakov
- Department for Molecular Evolution and Development, University of Vienna, Austria
| |
Collapse
|
14
|
Population co-divergence in common cuttlefish (Sepia officinalis) and its dicyemid parasite in the Mediterranean Sea. Sci Rep 2019; 9:14300. [PMID: 31586090 PMCID: PMC6778094 DOI: 10.1038/s41598-019-50555-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022] Open
Abstract
Population structure and biogeography of marine organisms are formed by different drivers than in terrestrial organisms. Yet, very little information is available even for common marine organisms and even less for their associated parasites. Here we report the first analysis of population structure of both a cephalopod host (Sepia officinalis) and its dicyemid parasite, based on a homologous molecular marker (cytochrome oxidase I). We show that the population of common cuttlefish in the Mediterranean area is fragmented into subpopulations, with some areas featuring restricted level of gene flow. Amongst the studied areas, Sardinia was genetically the most diverse and Cyprus the most isolated. At a larger scale, across the Mediterranean, the population structure of the parasite shows co-diversification pattern with its host, but a slower rate of diversification. Differences between the two counterparts are more obvious at a finer scale, where parasite populations show increased level of fragmentation and lower local diversities. This discrepancy can be caused by local extinctions and replacements taking place more frequently in the dicyemid populations, due to their parasitic lifestyle.
Collapse
|
15
|
The use of spatially explicit genetic variation data from four deep-sea sponges to inform the protection of Vulnerable Marine Ecosystems. Sci Rep 2019; 9:5482. [PMID: 30940897 PMCID: PMC6445101 DOI: 10.1038/s41598-019-41877-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 03/20/2019] [Indexed: 11/12/2022] Open
Abstract
The United Nations General Assembly has called for greater protection of the world’s deep-sea species and of features such as Vulnerable Marine Ecosystems (VMEs). Sponges are important components of VMEs and information about their spatially explicit genetic diversity can inform management decisions concerning the placement of protected areas. We employed a spatially explicit hierarchical testing framework to examine genetic variation amongst archived samples of four deep-sea sponges in the New Zealand region. For Poecillastra laminaris Sollas 1886, significant mitochondrial (COI, Cytb) and nuclear DNA (microsatellite) genetic differences were observed between provinces, amongst north-central-south regions and amongst geomorphic features. For Penares sp. no significant structure was detected (COI, 12S) across the same areas. For both Neoaulaxinia persicum Kelly, 2007 (COI, 12S) and Pleroma menoui Lévi & Lévi 1983 (COI) there was no evidence of genetic differentiation within their northern only regional distributions. Of 10 separate species-by-marker tests for isolation-by-distance and isolation-by-depth, only the isolation-by-depth test for N. persicum for COI was significant. The use of archived samples highlights how historical material may be used to support national and international management decisions. The results are discussed in the broader context of existing marine protected areas, and possible future design of spatial management measures for protecting VMEs in the New Zealand region.
Collapse
|
16
|
Nykänen M, Dillane E, Englund A, Foote AD, Ingram SN, Louis M, Mirimin L, Oudejans M, Rogan E. Quantifying dispersal between marine protected areas by a highly mobile species, the bottlenose dolphin, Tursiops truncatus. Ecol Evol 2018; 8:9241-9258. [PMID: 30377497 PMCID: PMC6194238 DOI: 10.1002/ece3.4343] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/19/2023] Open
Abstract
The functioning of marine protected areas (MPAs) designated for marine megafauna has been criticized due to the high mobility and dispersal potential of these taxa. However, dispersal within a network of small MPAs can be beneficial as connectivity can result in increased effective population size, maintain genetic diversity, and increase robustness to ecological and environmental changes making populations less susceptible to stochastic genetic and demographic effects (i.e., Allee effect). Here, we use both genetic and photo-identification methods to quantify gene flow and demographic dispersal between MPAs of a highly mobile marine mammal, the bottlenose dolphin Tursiops truncatus. We identify three populations in the waters of western Ireland, two of which have largely nonoverlapping core coastal home ranges and are each strongly spatially associated with specific MPAs. We find high site fidelity of individuals within each of these two coastal populations to their respective MPA. We also find low levels of demographic dispersal between the populations, but it remains unclear whether any new gametes are exchanged between populations through these migrants (genetic dispersal). The population sampled in the Shannon Estuary has a low estimated effective population size and appears to be genetically isolated. The second coastal population, sampled outside of the Shannon, may be demographically and genetically connected to other coastal subpopulations around the coastal waters of the UK. We therefore recommend that the methods applied here should be used on a broader geographically sampled dataset to better assess this connectivity.
Collapse
Affiliation(s)
- Milaja Nykänen
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Eileen Dillane
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Anneli Englund
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Andrew D. Foote
- School of Biological SciencesMolecular Ecology Fisheries Genetics LabBangor UniversityBangorUK
| | - Simon N. Ingram
- School of Biological and Marine SciencesPlymouth UniversityPlymouthUK
| | - Marie Louis
- Centre d'Etudes Biologiques de ChizéUMR 7372CNRS‐Université de La RochelleLa RochelleFrance
- Observatoire PelagisUMS 3462CNRS‐Université de La RochelleLa RochelleFrance
- Scottish Oceans InstituteUniversity of St AndrewsSt AndrewsUK
| | - Luca Mirimin
- Department of Natural SciencesSchool of Science and ComputingGalway‐Mayo Institute of TechnologyMarine and Freshwater Research CentreGalwayIreland
| | | | - Emer Rogan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| |
Collapse
|
17
|
Bishop CR, Hughes JM, Schmidt DJ. Mitogenomic analysis of the Australian lungfish (Neoceratodus forsteri) reveals structuring of indigenous riverine populations and late Pleistocene movement between drainage basins. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1034-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
18
|
Liu YC, Liu TH, Yu CC, Su CH, Chiao CC. Mismatch between the eye and the optic lobe in the giant squid. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170289. [PMID: 28791156 PMCID: PMC5541551 DOI: 10.1098/rsos.170289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Giant squids (Architeuthis) are a legendary species among the cephalopods. They live in the deep sea and are well known for their enormous body and giant eyes. It has been suggested that their giant eyes are not adapted for the detection of either mates or prey at distance, but rather are best suited for monitoring very large predators, such as sperm whales, at distances exceeding 120 m and at a depth below 600 m (Nilsson et al. 2012 Curr. Biol.22, 683-688. (doi:10.1016/j.cub.2012.02.031)). However, it is not clear how the brain of giant squids processes visual information. In this study, the optic lobe of a giant squid (Architeuthis dux, male, mantle length 89 cm), which was caught by local fishermen off the northeastern coast of Taiwan, was scanned using high-resolution magnetic resonance imaging in order to examine its internal structure. It was evident that the volume ratio of the optic lobe to the eye in the giant squid is much smaller than that in the oval squid (Sepioteuthis lessoniana) and the cuttlefish (Sepia pharaonis). Furthermore, the cell density in the cortex of the optic lobe is significantly higher in the giant squid than in oval squids and cuttlefish, with the relative thickness of the cortex being much larger in Architeuthis optic lobe than in cuttlefish. This indicates that the relative size of the medulla of the optic lobe in the giant squid is disproportionally smaller compared with these two cephalopod species. This morphological study of the giant squid brain, though limited only to the optic lobe, provides the first evidence to support that the optic lobe cortex, the visual information processing area in cephalopods, is well developed in the giant squid. In comparison, the optic lobe medulla, the visuomotor integration centre in cephalopods, is much less developed in the giant squid than other species. This finding suggests that, despite the giant eye and a full-fledged cortex within the optic lobe, the brain of giant squids has not evolved proportionally in terms of performing complex tasks compared with shallow-water cephalopod species.
Collapse
Affiliation(s)
- Yung-Chieh Liu
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Tsung-Han Liu
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Chun-Chieh Yu
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan, Republic of China
| | - Chia-Hao Su
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan, Republic of China
| | - Chuan-Chin Chiao
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| |
Collapse
|
19
|
Paxton CGM. Unleashing the Kraken: on the maximum length in giant squid (
Architeuthis
sp.). J Zool (1987) 2016. [DOI: 10.1111/jzo.12347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C. G. M. Paxton
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews UK
| |
Collapse
|
20
|
Ouvrard P, Hicks DM, Mouland M, Nicholls JA, Baldock KCR, Goddard MA, Kunin WE, Potts SG, Thieme T, Veromann E, Stone GN. Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus. Genome 2016; 59:1101-1116. [PMID: 27824505 DOI: 10.1139/gen-2016-0020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.
Collapse
Affiliation(s)
- Pierre Ouvrard
- a Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3JT, UK.,b Earth and Life Institute - Agronomy, Université catholique de Louvain, Place Croix du Sud 2, 1348 Louvain-la-Neuve, Belgium
| | - Damien M Hicks
- a Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3JT, UK
| | - Molly Mouland
- a Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3JT, UK
| | - James A Nicholls
- a Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3JT, UK
| | - Katherine C R Baldock
- c School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQUG, UK.,d Cabot Institute, University of Bristol, Woodland Road, Bristol, BS8 1UJ, UK
| | - Mark A Goddard
- e School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - William E Kunin
- e School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon G Potts
- f Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
| | - Thomas Thieme
- g BTL Bio-Test Labor GmbH Sagerheide, Kirchstrasse 3, D-18184 Thulendorf, Germany
| | - Eve Veromann
- h Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51014, Estonia
| | - Graham N Stone
- a Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3JT, UK
| |
Collapse
|
21
|
Alexander A, Steel D, Hoekzema K, Mesnick SL, Engelhaupt D, Kerr I, Payne R, Baker CS. What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)? Mol Ecol 2016; 25:2754-72. [DOI: 10.1111/mec.13638] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/06/2016] [Accepted: 03/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Alana Alexander
- Marine Mammal Institute; Hatfield Marine Science Center; Oregon State University; 2030 SE Marine Science Drive Newport OR 97365 USA
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
- Biodiversity Institute; University of Kansas; 1345 Jayhawk Blvd Lawrence KS 66045 USA
| | - Debbie Steel
- Marine Mammal Institute; Hatfield Marine Science Center; Oregon State University; 2030 SE Marine Science Drive Newport OR 97365 USA
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
| | - Sarah L. Mesnick
- Southwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | | | - Iain Kerr
- Ocean Alliance; 32 Horton Street Gloucester MA 01930 USA
| | - Roger Payne
- Ocean Alliance; 32 Horton Street Gloucester MA 01930 USA
| | - C. Scott Baker
- Marine Mammal Institute; Hatfield Marine Science Center; Oregon State University; 2030 SE Marine Science Drive Newport OR 97365 USA
- Department of Fisheries and Wildlife; Oregon State University; 104 Nash Hall Corvallis OR 97330 USA
- School of Biological Sciences; University of Auckland; Private Bag 92019 Auckland 1142 New Zealand
| |
Collapse
|
22
|
Ren J, Hou Z, Wang H, Sun MA, Liu X, Liu B, Guo X. Intraspecific Variation in Mitogenomes of Five Crassostrea Species Provides Insight into Oyster Diversification and Speciation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:242-254. [PMID: 26846524 DOI: 10.1007/s10126-016-9686-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
A large number of Crassostrea oysters are found in Asia-Pacific. While analyses of interspecific variation have helped to establish historical relationships among these species, studies on intraspecific variation are necessary to understand their recent evolutionary history and current forces driving population biology. We resequenced 18 and analyzed 31 mitogenomes of five Crassostrea species from China: Crassostrea gigas, Crassostrea angulata, Crassostrea sikamea, Crassostrea ariakensis, and Crassostrea hongkongensis. Our analysis finds abundant insertions, deletions, and single-nucleotide polymorphisms in all species. Intraspecific variation varies greatly among species with polymorphic sites ranging from 54 to 293 and nucleotide diversity ranging from 0.00106 to 0.00683. In all measurements, C. hongkongensis that has the narrowest geographic distribution exhibits the least sequence diversity; C. ariakensis that has the widest distribution shows the highest diversity, and species with intermediate distribution show intermediate levels of diversity. Low sequence diversity in C. hongkongensis may reflect recent bottlenecks that are probably exacerbated by human transplantation. High diversity in C. ariakensis is likely due to divergence of northern and southern China populations that have been separated without gene flow. The significant differences in mitogenome diversity suggest that the five sister species of Crassostrea have experienced different evolutionary forces since their divergence. The recent divergence of two C. ariakensis populations and the C. gigas/angulata species complex provides evidence for continued diversification and speciation of Crassostrea species along China's coast, which are shaped by unknown mechanisms in a north-south divide.
Collapse
Affiliation(s)
- Jianfeng Ren
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhanhui Hou
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Haiyan Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Ming-An Sun
- Epigenomics and Computational Biology Lab, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24060, USA
| | - Xiao Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Bin Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
| |
Collapse
|
23
|
Thompson KF, Patel S, Baker CS, Constantine R, Millar CD. Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean. Heredity (Edinb) 2015; 116:277-85. [PMID: 26626574 DOI: 10.1038/hdy.2015.99] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat.
Collapse
Affiliation(s)
- K F Thompson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,The Allan Wilson Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - S Patel
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,The Allan Wilson Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - C S Baker
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Fisheries and Wildlife and Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - R Constantine
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - C D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,The Allan Wilson Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| |
Collapse
|
24
|
Richter S, Schwarz F, Hering L, Böggemann M, Bleidorn C. The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae). Genome Biol Evol 2015; 7:3443-62. [PMID: 26590213 PMCID: PMC4700955 DOI: 10.1093/gbe/evv224] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glyceridae (Annelida) are a group of venomous annelids distributed worldwide from intertidal to abyssal depths. To trace the evolutionary history and complexity of glycerid venom cocktails, a solid backbone phylogeny of this group is essential. We therefore aimed to reconstruct the phylogenetic relationships of these annelids using Illumina sequencing technology. We constructed whole-genome shotgun libraries for 19 glycerid specimens and 1 outgroup species (Glycinde armigera). The chosen target genes comprise 13 mitochondrial proteins, 2 ribosomal mitochondrial genes, and 4 nuclear loci (18SrRNA, 28SrRNA, ITS1, and ITS2). Based on partitioned maximum likelihood as well as Bayesian analyses of the resulting supermatrix, we were finally able to resolve a robust glycerid phylogeny and identified three clades comprising the majority of taxa. Furthermore, we detected group II introns inside the cox1 gene of two analyzed glycerid specimens, with two different insertions in one of these species. Moreover, we generated reduced data sets comprising 10 million, 4 million, and 1 million reads from the original data sets to test the influence of the sequencing depth on assembling complete mitochondrial genomes from low coverage genome data. We estimated the coverage of mitochondrial genome sequences in each data set size by mapping the filtered Illumina reads against the respective mitochondrial contigs. By comparing the contig coverage calculated in all data set sizes, we got a hint for the scalability of our genome skimming approach. This allows estimating more precisely the number of reads that are at least necessary to reconstruct complete mitochondrial genomes in Glyceridae and probably non-model organisms in general.
Collapse
Affiliation(s)
- Sandy Richter
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany
| | - Francine Schwarz
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany
| | - Lars Hering
- Animal Evolution & Development, Institute of Biology, University of Leipzig, Germany Department of Zoology, Institute of Biology, University of Kassel, Germany
| | | | - Christoph Bleidorn
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| |
Collapse
|
25
|
Garrick RC, Bonatelli IAS, Hyseni C, Morales A, Pelletier TA, Perez MF, Rice E, Satler JD, Symula RE, Thomé MTC, Carstens BC. The evolution of phylogeographic data sets. Mol Ecol 2015; 24:1164-71. [DOI: 10.1111/mec.13108] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/21/2015] [Accepted: 02/04/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Ryan C. Garrick
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
| | - Isabel A. S. Bonatelli
- Departamento de Biologia; Universidade Federal de São Carlos; Campus Sorocaba Caixa Postal 18052780 Sorocaba São Paulo Brazil
| | - Chaz Hyseni
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
| | - Ariadna Morales
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Tara A. Pelletier
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Manolo F. Perez
- Departamento de Biologia; Universidade Federal de São Carlos; Campus Sorocaba Caixa Postal 18052780 Sorocaba São Paulo Brazil
| | - Edwin Rice
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Jordan D. Satler
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Rebecca E. Symula
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
| | - Maria Tereza C. Thomé
- Departamento de Zoologia; Instituto de Biociências; UNESP - Univ Estadual Paulista; Campus Rio Claro Caixa Postal 19913506-900 Rio Claro São Paulo Brazil
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| |
Collapse
|
26
|
McClain CR, Balk MA, Benfield MC, Branch TA, Chen C, Cosgrove J, Dove ADM, Gaskins L, Helm RR, Hochberg FG, Lee FB, Marshall A, McMurray SE, Schanche C, Stone SN, Thaler AD. Sizing ocean giants: patterns of intraspecific size variation in marine megafauna. PeerJ 2015; 3:e715. [PMID: 25649000 PMCID: PMC4304853 DOI: 10.7717/peerj.715] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/10/2014] [Indexed: 11/20/2022] Open
Abstract
What are the greatest sizes that the largest marine megafauna obtain? This is a simple question with a difficult and complex answer. Many of the largest-sized species occur in the world’s oceans. For many of these, rarity, remoteness, and quite simply the logistics of measuring these giants has made obtaining accurate size measurements difficult. Inaccurate reports of maximum sizes run rampant through the scientific literature and popular media. Moreover, how intraspecific variation in the body sizes of these animals relates to sex, population structure, the environment, and interactions with humans remains underappreciated. Here, we review and analyze body size for 25 ocean giants ranging across the animal kingdom. For each taxon we document body size for the largest known marine species of several clades. We also analyze intraspecific variation and identify the largest known individuals for each species. Where data allows, we analyze spatial and temporal intraspecific size variation. We also provide allometric scaling equations between different size measurements as resources to other researchers. In some cases, the lack of data prevents us from fully examining these topics and instead we specifically highlight these deficiencies and the barriers that exist for data collection. Overall, we found considerable variability in intraspecific size distributions from strongly left- to strongly right-skewed. We provide several allometric equations that allow for estimation of total lengths and weights from more easily obtained measurements. In several cases, we also quantify considerable geographic variation and decreases in size likely attributed to humans.
Collapse
Affiliation(s)
- Craig R McClain
- National Evolutionary Synthesis Center , Durham, NC , USA ; Department of Biology, Duke University , Durham, NC , USA
| | - Meghan A Balk
- Department of Biology, University of New Mexico , Albuquerque, NM , USA
| | - Mark C Benfield
- Department of Oceanography and Coastal Sciences, Louisiana State University , Baton Rouge, LA , USA
| | - Trevor A Branch
- School of Aquatic & Fishery Sciences, University of Washington , Seattle, WA , USA
| | - Catherine Chen
- Department of Biology, Duke University , Durham, NC , USA
| | - James Cosgrove
- Natural History Section, Royal British Columbia Museum , Victoria, BC , Canada
| | | | - Leo Gaskins
- Department of Biology, Duke University , Durham, NC , USA
| | - Rebecca R Helm
- Department of Ecology and Evolutionary Biology, Brown University , Providence, RI , USA
| | - Frederick G Hochberg
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History , Santa Barbara, CA , USA
| | - Frank B Lee
- Department of Biology, Duke University , Durham, NC , USA
| | | | - Steven E McMurray
- Department of Biology and Marine Biology, University of North Carolina Wilmington , Wilmington, NC , USA
| | | | - Shane N Stone
- Department of Biology, Duke University , Durham, NC , USA
| | - Andrew D Thaler
- Blackbeard Biologic: Science and Environmental Advisors , Vallejo, CA , USA
| |
Collapse
|
27
|
|
28
|
Morinha F, Clemente C, Cabral JA, Lewicka MM, Travassos P, Carvalho D, Dávila JA, Santos M, Blanco G, Bastos E. Next-generation sequencing and comparative analysis of Pyrrhocorax pyrrhocorax and Pyrrhocorax graculus (Passeriformes: Corvidae) mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2278-81. [PMID: 25431821 DOI: 10.3109/19401736.2014.984179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genomes of Red-billed Chough (Pyrrhocorax pyrrhocorax) and Yellow-billed Chough (Pyrrhocorax graculus) were sequenced using the Ion Torrent PGM platform. These mitogenomes contain 16,889 bp (Red-billed Chough) and 16,905 bp (Yellow-billed Chough), including 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (D-loop). The gene content, orientation, and structure are similar to a wide range of other vertebrate species and the nucleotide composition is very similar to other Passeriformes. All PCGs start with ATG, except for COX1 that starts with GTG, and four stop codons and one incomplete stop codon are used (TAA, TAG, AGG, AGA, and T-). The size of PCGs is the same in both mitogenomes, except for ND6 that has one codon less in the Yellow-billed Chough. All the tRNAs can fold into a typical cloverleaf secondary structure. These mitogenomic data can be of great value in complementing forthcoming approaches on molecular ecology, comparative and functional genomics.
Collapse
Affiliation(s)
- Francisco Morinha
- a Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD) , Vila Real , Portugal .,b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Carla Clemente
- c STAB VIDA, Madan Parque, Rua dos Inventores , Caparica , Portugal
| | - João A Cabral
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | | | - Paulo Travassos
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Diogo Carvalho
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - José A Dávila
- d Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC, UCLM, JCCM) , Ciudad Real , Spain , and
| | - Mário Santos
- b Laboratory of Applied Ecology , Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | | | - Estela Bastos
- a Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro (IBB/CGB-UTAD) , Vila Real , Portugal
| |
Collapse
|
29
|
Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL. Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesialonginaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. Zookeys 2014:271-88. [PMID: 25561842 PMCID: PMC4283376 DOI: 10.3897/zookeys.457.6569] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/21/2014] [Indexed: 11/12/2022] Open
Abstract
Artemesialonginaris is a marine shrimp endemic to the southwestern Atlantic and distributed from Atafona, Rio de Janeiro (Brazil) to Rawson, Chubut (Argentina). In recent years, this species has become an important target of the commercial fishery as a consequence of the decline in the fishery of more traditional and profitable marine shrimps. In addition, phenotypic variations have been documented in populations along its distribution. Therefore, investigations on the genetics of the fishing stocks are necessary for the development of sustainable management strategies and for understanding the possible sources of these variations. The mitochondrial gene Cytochrome Oxidase I (COI) was used to search for evidence of genetic structure among the populations of Artemesialonginaris and to analyze the phylogenetic relationships among them. A total of 60 specimens were collected from seven different localities, covering its geographical range. The final alignment showed 53 haplotypes (48 individuals and 5 shared), with no biogeographical pattern. The low genetic divergence found, with a non-significant FST value, also suggests the absence of population structure for this gene. These findings indicate a continuous gene flow among the populations analyzed, suggesting that the phenotypic variation is a consequence of different environmental conditions among the localities.
Collapse
Affiliation(s)
- Abner Carvalho-Batista
- Laboratory of Biology of Marine and Fresh Water Shrimps, Faculty of Science, Department of Biological Sciences, São Paulo State University (UNESP), Bauru, São Paulo, Brazil
| | - Mariana Negri
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
| | - Leonardo G Pileggi
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
| | - Antonio L Castilho
- São Paulo State University (UNESP), Biosciences Institute of Botucatu, Zoology Department, Botucatu, Brazil
| | - Rogério C Costa
- Laboratory of Biology of Marine and Fresh Water Shrimps, Faculty of Science, Department of Biological Sciences, São Paulo State University (UNESP), Bauru, São Paulo, Brazil
| | - Fernando L Mantelatto
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
| |
Collapse
|
30
|
Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing. BMC Evol Biol 2014; 14:232. [PMID: 25406508 PMCID: PMC4245800 DOI: 10.1186/s12862-014-0232-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/04/2014] [Indexed: 11/23/2022] Open
Abstract
Background Mitochondrial DNA markers have long been used to identify population boundaries and are now a standard tool in conservation biology. In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with commonly used control region sequencing or other single gene approaches. In this study we sequenced the whole mitogenome of 93 Critically Endangered Speartooth Shark Glyphis glyphis from the last three river drainages they inhabit in northern Australia. Results Genetic diversity was extremely low (π =0.00019) but sufficient to demonstrate the existence of barriers to gene flow among river drainages (AMOVA ΦST =0.28283, P <0.00001). Surprisingly, the comparison with single gene sub-datasets revealed that ND5 and 12S were the only ones carrying enough information to detect similar levels of genetic structure. The control region exhibited only one mutation, which was not sufficient to detect any structure among river drainages. Conclusions This study strongly supports the use of single river drainages as discrete management units for the conservation of G. glyphis. Furthermore when genetic diversity is low, as is often the case in elasmobranchs, our results demonstrate a clear advantage of using the whole mitogenome to inform population structure compared to single gene approaches. More specifically, this study questions the extensive use of the control region as the preferential marker for elasmobranch population genetic studies and whole mitogenome sequencing will probably uncover a large amount of cryptic population structure in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0232-x) contains supplementary material, which is available to authorized users.
Collapse
|
31
|
Tsangaras K, Wales N, Sicheritz-Pontén T, Rasmussen S, Michaux J, Ishida Y, Morand S, Kampmann ML, Gilbert MTP, Greenwood AD. Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank). PLoS One 2014; 9:e109101. [PMID: 25275614 PMCID: PMC4183570 DOI: 10.1371/journal.pone.0109101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/29/2014] [Indexed: 11/23/2022] Open
Abstract
Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information.
Collapse
Affiliation(s)
- Kyriakos Tsangaras
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Johan Michaux
- Conservation Genetics Unit, Institute of Botany (Bat. 22), University of Liège, Liège, Belgium
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Serge Morand
- Institut des Sciences de l’Evolution, Université de Montpellier II, Montpellier Cedex 5, France
| | - Marie-Louise Kampmann
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- * E-mail:
| |
Collapse
|
32
|
Gillett CPDT, Crampton-Platt A, Timmermans MJTN, Jordal BH, Emerson BC, Vogler AP. Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Mol Biol Evol 2014; 31:2223-37. [PMID: 24803639 PMCID: PMC4104315 DOI: 10.1093/molbev/msu154] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based "bait" sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge.
Collapse
Affiliation(s)
- Conrad P D T Gillett
- Department of Life Sciences, Natural History Museum, London, United KingdomSchool of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United Kingdom
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Bjarte H Jordal
- The Natural History Museum, University Museum of Bergen, Bergen, Norway
| | - Brent C Emerson
- School of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United KingdomIsland Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, La Laguna, Tenerife, Canary Islands, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| |
Collapse
|
33
|
Allcock AL, Lindgren A, Strugnell J. The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review. J NAT HIST 2014. [DOI: 10.1080/00222933.2013.825342] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
34
|
Hoving HJT, Perez JAA, Bolstad KSR, Braid HE, Evans AB, Fuchs D, Judkins H, Kelly JT, Marian JEAR, Nakajima R, Piatkowski U, Reid A, Vecchione M, Xavier JCC. The study of deep-sea cephalopods. ADVANCES IN MARINE BIOLOGY 2014; 67:235-359. [PMID: 24880796 DOI: 10.1016/b978-0-12-800287-2.00003-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
"Deep-sea" cephalopods are here defined as cephalopods that spend a significant part of their life cycles outside the euphotic zone. In this chapter, the state of knowledge in several aspects of deep-sea cephalopod research are summarized, including information sources for these animals, diversity and general biogeography and life cycles, including reproduction. Recommendations are made for addressing some of the remaining knowledge deficiencies using a variety of traditional and more recently developed methods. The types of oceanic gear that are suitable for collecting cephalopod specimens and images are reviewed. Many groups of deep-sea cephalopods require taxonomic reviews, ideally based on both morphological and molecular characters. Museum collections play a vital role in these revisions, and novel (molecular) techniques may facilitate new use of old museum specimens. Fundamental life-cycle parameters remain unknown for many species; techniques developed for neritic species that could potentially be applied to deep-sea cephalopods are discussed. Reproductive tactics and strategies in deep-sea cephalopods are very diverse and call for comparative evolutionary and experimental studies, but even in the twenty-first century, mature individuals are still unknown for many species. New insights into diet and trophic position have begun to reveal a more diverse range of feeding strategies than the typically voracious predatory lifestyle known for many cephalopods. Regular standardized deep-sea cephalopod surveys are necessary to provide insight into temporal changes in oceanic cephalopod populations and to forecast, verify and monitor the impacts of global marine changes and human impacts on these populations.
Collapse
Affiliation(s)
| | - Jose Angel A Perez
- Centro de Ciências Tecnológicas da Terra e do Mar Universidade do Vale do Itajaí, Itajaí, Santa Catarina, Brazil
| | - Kathrin S R Bolstad
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Heather E Braid
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Aaron B Evans
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Dirk Fuchs
- Freie Universität Berlin, Institute of Geological Sciences, Branch Paleontology, Berlin, Germany
| | - Heather Judkins
- Department of Biological Sciences, University of South Florida St. Petersburg, St. Petersburg, Florida, USA
| | - Jesse T Kelly
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - José E A R Marian
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
| | - Ryuta Nakajima
- Department of Art and Design, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Uwe Piatkowski
- GEOMAR, Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Amanda Reid
- Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Michael Vecchione
- NMFS National Systematics Laboratory, National Museum of Natural History, Washington, DC, USA
| | - José C C Xavier
- Institute of Marine Research, Department of Life Sciences, University of Coimbra, Coimbra, Portugal; British Antarctic Survey, NERC, Cambridge, United Kingdom
| |
Collapse
|