Recent speciation and hybridization in Icelandic deep‐sea isopods: An integrative approach using genomics and proteomics

Paulus, Eva; Brix, Saskia; Siebert, Annabelle; Arbizu, Pedro Martínez; Rossel, Sven; Peters, Janna; Svavarsson, Jörundur; Schwentner, Martin

doi:10.1111/mec.16234

Cited by 17 publications

(36 citation statements)

References 100 publications

(160 reference statements)

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“…Five individuals of each species were studied, where available. Haploniscus bicuspis has been previously shown to represent a species complex (see Paulus et al, 2021) To identify genetic lineages that may correspond to species, two different computational approaches were employed: general mixed Yule coalescent (GMYC; Pons et al, 2006) and assembling species by automatic partitioning (ASAP; Puillandre et al, 2021). ASAP partitions species by ranked genetic distances.…”

Section: Cytrocrome Oxidase I Barcodingmentioning

confidence: 99%

“…Data were visualized using QGIS 3.4.7-Madeira (QGIS Development Team, 2020) with the WGS 84 (ESPG: 32631) coordinate reference system. Individuals of Halploniscus bicuspis were assigned to the three species found within the species complex in Paulus et al (2021) based on their distribution. To analyze the species' depth distribution, a box and whisker plots was created with Excel 16.53 (Microsoft Corporation, 2021).…”

Section: Geographical and Depth Distribution Of Haploniscidae Species Distributed Around Icelandmentioning

confidence: 99%

“…Species distribution models (SDM) were calculated using the random forest approach (Breiman, 2001). Random Forest is a non-parametric and non-linear modeling approach based on decision trees (Hastie et al, 2009), which has been successfully applied to the modeling of species distributions around Iceland in both classification (Meißner et al, 2014;Paulus et al, 2021) and regression problems (Ostmann and Arbizu, 2018).…”

Section: Species Distribution Modelsmentioning

confidence: 99%

“…Since the deep-sea environment also has a high proportion of morphologically similar but genetically different species, so-called cryptic species (Raupach and Wägele, 2006;Vrijenhoek, 2009;Brasier et al, 2016), the morphospecies approach tends to underestimate true biodiversity and, conversely, to overestimate the range of species and their population size. In addition, intraspecific morphological variability, including ontogenetic variation, polymorphism, or sexual dimorphism, poses a challenge to species assignment based on morphological characters alone (Raupach and Wägele, 2006;Riehl et al, 2012;Zaharias et al, 2020;Paulus et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…In the last two decades, major leaps have been made in the development of taxonomic approaches and methodologies, including DNA-based taxonomy and (meta-) barcoding, "-omic" techniques, imaging tools, and integrative approaches linking different types of taxonomic information (Dayrat, 2005;Boistel et al, 2011;Raupach et al, 2016;Paulus et al, 2021). Many of these methods, despite their apparent advantage in facilitating and accelerating species delimitation, have been slow to find their way into deep-sea taxonomy.…”

Section: Introductionmentioning

confidence: 99%

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Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

et al. 2022

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Correct identification of species is required to assess and understand the biodiversity of an ecosystem. In the deep sea, however, this is only possible to a limited extent, as a large part of the fauna is undescribed and the identification keys for most taxa are inadequate or missing. With the progressive impact of climate change and anthropogenic activities on deep-sea ecosystems, it is imperative to define reliable methods for robust species identification. In this study, different techniques for the identification of deep-sea species are tested, including a combination of morphological, molecular (DNA barcoding, and proteomic fingerprinting), biogeographical and ecological modeling approaches. These are applied to a family of isopods, the Haploniscidae, from deep waters around Iceland. The construction of interactive identification keys based on the DELTA format (DEscription Language for TAxonomy) were a major pillar of this study, the evaluation of which was underpinned by the application of the supplementary methods. Overall, interactive keys have been very reliable in identifying species within the Haploniscidae. Especially in a deep-sea context, these types of keys could become established because they are easy to adapt and flexible enough to accommodate newly described species. Remarkably, in this study, the interactive key enabled identification of a supposedly new species within the Haploniscidae that was later verified using both molecular genetic – and proteomic methods. However, these keys are limited given that they are based on purely morphological characteristics, including where species with strong ontogenetic or sexual dimorphism occur as both genders are not always described. In this case, integrative taxonomy is the method of choice and the combination presented here has been shown to be very promising for correct identification of deep-sea isopods.

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Section: Cytrocrome Oxidase I Barcodingmentioning

confidence: 99%

Section: Geographical and Depth Distribution Of Haploniscidae Species Distributed Around Icelandmentioning

confidence: 99%

Section: Species Distribution Modelsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

et al. 2022

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Evaluating species richness using proteomic fingerprinting and DNA barcoding—a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone

et al. 2022

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The Clarion Clipperton Fracture Zone (CCZ) is a vast deep-sea region harboring a highly diverse benthic fauna, which will be affected by potential future deep-sea mining of metal-rich polymetallic nodules. Despite the need for conservation plans and monitoring strategies in this context, the majority of taxonomic groups remain scientifically undescribed. However, molecular rapid assessment methods such as DNA barcoding and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) provide the potential to accelerate specimen identification and biodiversity assessment significantly in the deep-sea areas. In this study, we successfully applied both methods to investigate the diversity of meiobenthic copepods in the eastern CCZ, including the first application of MALDI-TOF MS for the identification of these deep-sea organisms. Comparing several different species delimitation tools for both datasets, we found that biodiversity values were very similar, with Pielou’s evenness varying between 0.97 and 0.99 in all datasets. Still, direct comparisons of species clusters revealed differences between all techniques and methods, which are likely caused by the high number of rare species being represented by only one specimen, despite our extensive dataset of more than 2000 specimens. Hence, we regard our study as a first approach toward setting up a reference library for mass spectrometry data of the CCZ in combination with DNA barcodes. We conclude that proteome fingerprinting, as well as the more established DNA barcoding, can be seen as a valuable tool for rapid biodiversity assessments in the future, even when no reference information is available.

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Diversity, distribution and composition of abyssal benthic Isopoda in a region proposed for deep-seafloor mining of polymetallic nodules: a synthesis

et al. 2023

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Due to the increasing challenge of meeting human demands for metals from land-based resources, interest in extracting mineral ores from the deep sea has gained momentum in recent years. Targeted mining of deep-seabed minerals could have adverse effects on the associated ecosystems, but knowledge on the biological communities found there, their structure and functions is still limited. The focus of this study is to provide an overview on isopod crustaceans from the Clarion Clipperton Fracture Zone (CCFZ), an area well-known for its abundance of high-grade polymetallic nodules. Isopods generally comprise an important part of the macrofaunal communities of soft deep-sea sediments and indeed are one of the most dominant macrobenthic groups in the CCFZ. In this review, we have compiled all available data and information on isopod diversity and distribution in the CCFZ in a hybrid manner, which includes published data from the literature as well as the analysis of previously unpublished sources and newly collected data. Although isopods are one of the more prevalent and better-known groups of the CCFZ fauna, this study shows that it is still remarkably difficult to obtain a clear perception of isopod diversity and distribution, as well as the factors that could be responsible for the observed patterns. In many places, knowledge remains incomplete, which is largely due to the low sampling and taxonomic effort, non-standardised sample protocols and the limited taxonomic inter-calibration between studies. The latter is pivotal due to the high proportion of undescribed and presumably new species that typically occur there. An important starting point would therefore be to increase sampling effort and its spatial and temporal coverage in a standardised way, to intensify (integrative) taxonomic work as well as to facilitate sample and data exchange between scientists and contractors. These are fundamental requirements to improve our understanding of the biodiversity of isopods, but also of other faunal groups, in the CCFZ, before mining operations begin.

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Recent speciation and hybridization in Icelandic deep‐sea isopods: An integrative approach using genomics and proteomics

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution-NonCo mmercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 17 publications

References 100 publications

Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

Evaluating species richness using proteomic fingerprinting and DNA barcoding—a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone

Diversity, distribution and composition of abyssal benthic Isopoda in a region proposed for deep-seafloor mining of polymetallic nodules: a synthesis

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