The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa

There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.

Amphipods as biomonitors of marine coastal environments: a Chatham Island case study

<p>New Zealand’s coastal marine environment has high economic, social and cultural importance. In order to manage, preserve and safely enjoy coastal environments and their resources, a good understanding of their biochemistry is required. Biomonitors provide a mechanism for monitoring changes in an environment especially in measuring metals entering the food chain. Trace metals are non-biodegradable, have the ability to become highly toxic to biota at relatively low concentrations, and bio-magnify up the food chain. Amphipods, a diverse order of crustacea, are widespread, abundant, relatively sedentary and important at the base of the food web. Furthermore, amphipods bioaccumulate pollutants through multiple sources, including seawater, sediment and their diet, and may thus provide a comprehensive insight into the chemistry of an environment. This study investigates the trace metal chemistry of amphipods and associated algae, seawater and sediment, from coastal marine sites around Chatham Island. Samples were obtained from 11 coastal localities with the sampling sites located near potential point pollutants and on distinct basement lithologies, as well as a site identified by Te Aitanga o Ngā Uri o Wharekauri as relatively pristine. Three algal-dwelling amphipods (Aora sp. 1, Apohyale sp. 1, Eusiroides sp. 1) and one sand hopper species (Bellorchestia chathamensis (Hurley, 1956)) were found to be the most abundant and ubiquitous species collected. Sites were prioritised based on the abundances of these amphipod species and samples were analysed for >35 trace elements. Spatial and interspecific variations were observed for all amphipod species investigated. Eusiroides sp. 1 was the most sensitive algal-dwelling amphipod species analysed and consistently had highest concentrations of trace metals at a given site. No size effect was found for most trace element concentrations in two amphipod species. All three algal-dwelling amphipod species and associated seawater samples from Hanson Point South had elevated concentrations for > 19 trace metals, including potentially ecotoxic trace metals such as Ti, V, Cr, Co, Ni, Cu, and Fe. Arsenic was elevated in the algal-dwelling amphipod species at Owenga and Cd at Kaingaroa West and Cape Pattisson. Trace metal concentrations in the algal-dwelling amphipod specimens were broadly reflected in their associated seawater and/or algae. However there were variations in this, with the Hanson Point South amphipods more closely matching seawater than algae concentration patterns, and the algae at Owenga not showing As elevations noted in the amphipods. This suggests amphipods accumulate metals from a variety of sources, both directly from seawater and variably from algae. Sediments appeared to have little influence on the trace metals bioaccumulated in the amphipod specimens. Results from this research demonstrate that species and size effects must be considered to rigorously use amphipods as biomonitors. Amphipods appear to provide a better insight to bio-available trace metal contamination compared to the other sample types analysed here. This thesis aids in the development and application of amphipods as biomonitors in New Zealand coastal waters and provides a baseline for sites located across Chatham Island for >30 trace elements. This baseline may be utilized by future studies to investigate temporal variations in trace metal concentrations on Chatham Island.</p>

Amphipods as biomonitors of marine coastal environments: a Chatham Island case study

<p>New Zealand’s coastal marine environment has high economic, social and cultural importance. In order to manage, preserve and safely enjoy coastal environments and their resources, a good understanding of their biochemistry is required. Biomonitors provide a mechanism for monitoring changes in an environment especially in measuring metals entering the food chain. Trace metals are non-biodegradable, have the ability to become highly toxic to biota at relatively low concentrations, and bio-magnify up the food chain. Amphipods, a diverse order of crustacea, are widespread, abundant, relatively sedentary and important at the base of the food web. Furthermore, amphipods bioaccumulate pollutants through multiple sources, including seawater, sediment and their diet, and may thus provide a comprehensive insight into the chemistry of an environment. This study investigates the trace metal chemistry of amphipods and associated algae, seawater and sediment, from coastal marine sites around Chatham Island. Samples were obtained from 11 coastal localities with the sampling sites located near potential point pollutants and on distinct basement lithologies, as well as a site identified by Te Aitanga o Ngā Uri o Wharekauri as relatively pristine. Three algal-dwelling amphipods (Aora sp. 1, Apohyale sp. 1, Eusiroides sp. 1) and one sand hopper species (Bellorchestia chathamensis (Hurley, 1956)) were found to be the most abundant and ubiquitous species collected. Sites were prioritised based on the abundances of these amphipod species and samples were analysed for >35 trace elements. Spatial and interspecific variations were observed for all amphipod species investigated. Eusiroides sp. 1 was the most sensitive algal-dwelling amphipod species analysed and consistently had highest concentrations of trace metals at a given site. No size effect was found for most trace element concentrations in two amphipod species. All three algal-dwelling amphipod species and associated seawater samples from Hanson Point South had elevated concentrations for > 19 trace metals, including potentially ecotoxic trace metals such as Ti, V, Cr, Co, Ni, Cu, and Fe. Arsenic was elevated in the algal-dwelling amphipod species at Owenga and Cd at Kaingaroa West and Cape Pattisson. Trace metal concentrations in the algal-dwelling amphipod specimens were broadly reflected in their associated seawater and/or algae. However there were variations in this, with the Hanson Point South amphipods more closely matching seawater than algae concentration patterns, and the algae at Owenga not showing As elevations noted in the amphipods. This suggests amphipods accumulate metals from a variety of sources, both directly from seawater and variably from algae. Sediments appeared to have little influence on the trace metals bioaccumulated in the amphipod specimens. Results from this research demonstrate that species and size effects must be considered to rigorously use amphipods as biomonitors. Amphipods appear to provide a better insight to bio-available trace metal contamination compared to the other sample types analysed here. This thesis aids in the development and application of amphipods as biomonitors in New Zealand coastal waters and provides a baseline for sites located across Chatham Island for >30 trace elements. This baseline may be utilized by future studies to investigate temporal variations in trace metal concentrations on Chatham Island.</p>

Global gap-analysis of amphipod barcode library

In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as “white gaps”. Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.

On the brink of extinction: a new freshwater amphipod Jesogammarus acalceolus (Anisogammaridae) from Japan

Freshwater habitats, especially cold springs, are environments in which the risk of extinction faced by organisms remains high due to human activities. To conserve endangered species, it is important to describe and name them. Here, a new, endangered freshwater anisogammarid amphipod species, Jesogammarus (Jesogammarus) acalceolussp. nov., found in a spring in Aomori Prefecture, Japan, is described which is potentially the sole remaining habitat of this species. Both morphological and molecular phylogenetic results strongly support the nesting of the new species within Jesogammarus. Jesogammarus (J.) acalceolussp. nov. is the first species of genus Jesogammarus that was found to lack a calceolus, a sensory organ located on male antenna 2. Thus, the diagnostic criteria for this genus required amendment. A reconstruction of ancestral calceoli, based on a molecular phylogenetic tree, revealed that the common ancestor of Jesogammarus possessed calceoli, which were secondarily lost in J. (J.) acalceolussp. nov. Our results indicate that this new species, which is key to clarifying the evolution of the calceolus, is of high conservation significance.

Influence of environmental factors and sessile biota on vagile epibionts: The case of amphipods in marinas across a regional scale

Marinas are highly anthropized environments, with singular ecological characteristics. In the present study the spatial variability of the amphipod assemblage associated to floating pontoons was analyzed. Moreover, the influence of the environmental data and the sessile biota on the amphipod assemblage structure were assessed. Six marinas were selected along the Southern Iberian Peninsula, three in the Atlantic and three in the Mediterranean, and three floating pontoons were sampled at each marina. Four-teen amphipod species were identified, most of them corresponded to detritivores and generalist species. Statistical analyses considering amphipod composition and abundance did not show significant differences between the Atlantic and the Mediterranean, but there were significant differences among marinas. Copper had a significant correlation with the amphipod assemblage. The sessile species Bugula neritina and Ellisolandia elongata also showed a significant influence on the spatial patterns of the amphipod assemblages. Therefore, environmental conditions and sessile composition seem to affect, simultaneously, the spatial variability of amphipod assemblage associated to floating pontoons in marinas. Both factors are key to understand the singularity of marinas. This fact should be taken into consideration to prevent the use of a single management program in these environments.