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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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Leggett MA, Vink CJ, Nelson XJ. Adaptation and Survival of Marine-Associated Spiders (Araneae). ANNUAL REVIEW OF ENTOMOLOGY 2024; 69:481-501. [PMID: 37788437 DOI: 10.1146/annurev-ento-062923-102457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Aquatic environments are an unusual habitat for most arthropods. Nevertheless, many arthropod species that were once terrestrial dwelling have transitioned back to marine and freshwater environments, either as semiaquatic or, more rarely, as fully aquatic inhabitants. Transition to water from land is exceptional, and without respiratory modifications to allow for extended submergence and the associated hypoxic conditions, survival is limited. In this article, we review marine-associated species that have made this rare transition in a generally terrestrial group, spiders. We include several freshwater spider species for comparative purposes. Marine-associated spiders comprise less than 0.3% of spider species worldwide but are found in over 14% of all spider families. As we discuss, these spiders live in environments that, with tidal action, hydraulic forces, and saltwater, are more extreme than freshwater habitats, often requiring physiological and behavioral adaptations to survive. Spiders employ many methods to survive inundation from encroaching tides, such as air bubble respiration, airtight nests, hypoxic comas, and fleeing incoming tides. While airway protection is the primary survival strategy, further survival adaptations include saltwater-induced osmotic regulation, dietary composition, predator avoidance, reproduction, locomotory responses, and adaptation to extreme temperatures and hydrostatic pressures that challenge existence in marine environments.
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Affiliation(s)
- Marlene A Leggett
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand;
| | - Cor J Vink
- Department of Pest Management and Conservation, Lincoln University, Lincoln, New Zealand
| | - Ximena J Nelson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand;
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Kulkarni S, Wood HM, Hormiga G. Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies. Cladistics 2023; 39:479-532. [PMID: 37787157 DOI: 10.1111/cla.12557] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter-relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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The Effect of Sampling Bias on Evaluating the Diversity and Distribution Patterns of Iranian Spiders (Arachnida: Araneae). DIVERSITY 2022. [DOI: 10.3390/d15010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although spiders constitute a highly diversified group of animals, the knowledge regarding their geographic distribution (i.e., the so-called Wallacean shortfall) and diversity patterns is incipient on a global scale; while attempts to explore such patterns have been made for the highly diversified Neotropical fauna, several Old World regions are historically neglected. Aiming to close this gap, the present study provides the most comprehensive review of spatial variation in the diversity patterns of the spider fauna of Iran. We also examined the effects of sampling biases on the results. We gathered a database with 4434 non-duplicate records of 935 species of spiders from Iran, 215 of which are currently considered endemic to the country. We showed that, despite a significant improvement in state-of-the-art taxonomic research regarding this fauna in the past 20 years, the Iranian spider fauna suffers from a highly uneven distribution of records throughout the country and its ecoregions. Additionally, highly sampled areas are typically near large cities. We also found a high correlation between the number of records and species of spiders and the number of records of plants and other animals in Iran, suggesting that the biodiversity shortfalls herein described for spiders are corroborated by other taxa. The biases reported herein are likely to be observed for other countries, as the area alone explained only 33.24% of the spider species richness among 171 compared countries. We hope that the present study stimulates further sampling and research aiming to explore this fauna and the underlying biological processes related to its patterns of diversity and distribution.
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Marusik YM. On the three poorly known species of Dictyna Sundevall, 1833 (Araneae: Dictynidae) described from Armenia and Siberia. J NAT HIST 2022. [DOI: 10.1080/00222933.2022.2073479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Yuri M. Marusik
- Institute for Biological Problems of the North, Magadan, Russia
- Department of Zoology & Entomology, University of the Free State, Bloemfontein, South Africa
- Zoological Museum, Biodiversity Unit, University of Turku, Finland
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Albín A, González M, Simó M, Kossyrczyk EW, Bidegaray‐Batista L, Aisenberg A. Eight‐legged swimmers: Behavioral responses to floods in two South American spiders. Ethology 2021. [DOI: 10.1111/eth.13235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Albín
- Departamento de Ecología y Biología Evolutiva Instituto de Investigaciones Biológicas Clemente Estable Montevideo Uruguay
- Sección Entomología Facultad de Ciencias Universidad de la República Montevideo Uruguay
| | - Macarena González
- Departamento de Ecología y Biología Evolutiva Instituto de Investigaciones Biológicas Clemente Estable Montevideo Uruguay
- Departamento de Biodiversidad y Genética Instituto de Investigaciones Biológicas Clemente Montevideo Uruguay
| | - Miguel Simó
- Sección Entomología Facultad de Ciencias Universidad de la República Montevideo Uruguay
| | - Elizabeth W. Kossyrczyk
- Departamento de Ecología y Biología Evolutiva Instituto de Investigaciones Biológicas Clemente Estable Montevideo Uruguay
| | - Leticia Bidegaray‐Batista
- Departamento de Biodiversidad y Genética Instituto de Investigaciones Biológicas Clemente Montevideo Uruguay
| | - Anita Aisenberg
- Departamento de Ecología y Biología Evolutiva Instituto de Investigaciones Biológicas Clemente Estable Montevideo Uruguay
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Li F, Bian C, Li D, Shi Q. Spider Silks: An Overview of Their Component Proteins for Hydrophobicity and Biomedical Applications. Protein Pept Lett 2021; 28:255-269. [PMID: 32895035 DOI: 10.2174/0929866527666200907104401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/22/2022]
Abstract
Spider silks have received extensive attention from scientists and industries around the world because of their remarkable mechanical properties, which include high tensile strength and extensibility. It is a leading-edge biomaterial resource, with a wide range of potential applications. Spider silks are composed of silk proteins, which are usually very large molecules, yet many silk proteins still remain largely underexplored. While there are numerous reviews on spider silks from diverse perspectives, here we provide a most up-to-date overview of the spider silk component protein family in terms of its molecular structure, evolution, hydrophobicity, and biomedical applications. Given the confusion regarding spidroin naming, we emphasize the need for coherent and consistent nomenclature for spidroins and provide recommendations for pre-existing spidroin names that are inconsistent with nomenclature. We then review recent advances in the components, identification, and structures of spidroin genes. We next discuss the hydrophobicity of spidroins, with particular attention on the unique aquatic spider silks. Aquatic spider silks are less known but may inspire innovation in biomaterials. Furthermore, we provide new insights into antimicrobial peptides from spider silk glands. Finally, we present possibilities for future uses of spider silks.
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Affiliation(s)
- Fan Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Chao Bian
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Daiqin Li
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
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Li F, Lv Y, Wen Z, Bian C, Zhang X, Guo S, Shi Q, Li D. The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders. BMC Ecol Evol 2021; 21:72. [PMID: 33931054 PMCID: PMC8086345 DOI: 10.1186/s12862-021-01803-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/22/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. RESULTS We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. CONCLUSIONS Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.
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Affiliation(s)
- Fan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083 China
- Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, 430062 Hubei China
| | - Yunyun Lv
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100 China
| | - Zhengyong Wen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083 China
| | - Chao Bian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083 China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083 China
| | - Shengtao Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083 China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, 518083 China
| | - Daiqin Li
- Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
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