Patterns of population genetic structure and connectivity of squat lobsters associated with vulnerable marine ecosystems

<p>Vulnerable marine ecosystems (VMEs) are susceptible to the impact of intense or long-term anthropogenic activities (e.g., bottom trawling). Networks of marine protected areas (MPAs) can help facilitate the conservation and restoration of biodiversity and ecosystem function provided by VMEs. An understanding of the connectivity amongst populations of deep-sea organisms is crucial for informing the management of VMEs, by assessing the effectiveness of existing MPAs and informing the placement of new MPAs. Genetic evaluation of population structure is one of the most commonly used indirect approaches for interpreting connectivity. In contrast to corals or sponges, which are typically habitat-forming organisms as VME-indicator taxa, squat lobsters are often found in close association with VMEs and can be considered to be VME-associated taxa. Nowadays, population genetic studies of deep-sea fauna mainly focus on VME-indicator taxa, whilst relatively few studies have focussed on VME-associated taxa, such as squat lobsters, whose distribution is not exclusively limited to VMEs. In this study, three deep-sea squat lobster species, Munida isos Ahyong & Poore, 2004, Munida endeavourae Ahyong & Poore, 2004 and Munida gracilis Henderson, 1885, were selected based on their association with VMEs (e.g., cold-water coral reefs and seamounts), wide distributional ranges across the southwest Pacific Ocean, and sample availability. The overall aims of this research are to evaluate patterns of population structure and genetic connectivity of three squat lobster taxa in the southwest Pacific Ocean and consider how the acquired genetic information can contribute to the management and conservation of VMEs in the southwest Pacific Ocean. A general introduction of VMEs, MPAs, connectivity of deep-sea fauna, High-Throughput Sequencing (HTS), study area and study taxa are presented in Chapter 1. To provide background information for this research, a review was conducted of the molecular-based studies of the systematics, taxonomy and phylogenetics of marine squat lobster taxa (Chapter 2). Recent molecular-based studies have dramatically increased our understanding of squat lobster phylogenetics and systematics, and thereby the taxonomy of this diverse and challenging group, which provide a valuable starting point for evaluating hypotheses concerning speciation, biogeography, adaptation and co-evolution (e.g., squat lobsters and corals). Notably, accurate taxonomy is critical for population genetic studies and consequently supports the conservation efforts of VMEs. A range of molecular genetic markers, including the mitochondrial COI region, nuclear microsatellites and single nucleotide polymorphisms (SNPs), were utilised to evaluate the genetic connectivity amongst populations of three VME-associated taxa (Munida isos, M. endeavourae and M. gracilis). In addition to this, universal invertebrate primers were used to yield partial COI fragments of 649 bp (DNA barcoding) for the three Munida species to confirm the taxonomic identity and to exclude the possibility of cryptic species. Due to limited genetic information for the three Munida species, novel microsatellite loci were developed for M. isos based on the HiSeq 2500 sequencing platform and used for cross-species amplification in M. endeavourae and M. gracilis (Chapter 3). Additionally, a Genotyping by Sequencing (GBS) protocol and the Universal Network Enabled Analysis Kit (UNEAK) pipeline were employed to develop novel SNPs for M. isos samples from the southwest Pacific Ocean (Chapter 5). A spatially explicit hierarchical testing framework (Northern-Southern biogeographical provinces, North-Central-South regions, and individual geomorphic features) was employed for the evaluation of connectivity amongst populations of the three deep-sea squat lobster taxa across their distributional range in the southwest Pacific Ocean (Chapter 4). The level of genetic diversity was high as revealed by variation at the COI region, and moderate based on microsatellite markers across the three Munida species. With more than 96% of the variance being attributed to differences within populations in the three Munida species, based on both marker types, no genetic subdivision was detected in M. endeavourae, whilst little genetic differentiation was observed in M. isos and M. gracilis based on microsatellite variation. For M. isos, populations from the Tasmanian slope were potentially genetically different from all other populations and may act as source populations, whereas populations from the Kermadec Ridge may be sink populations. Robust evidence of recent demographic expansions was detected in the three Munida species, based on COI and microsatellite marker types. The estimated time of demographic expansions for the three Munida species was ca. 16.1 kya, 24.4 kya and 21.6 kya for the M. isos, M. endeavourae and M. gracilis, respectively, coinciding with the late Pleistocene. The results are discussed in the context of the distribution of existing MPAs, and contribute new information useful to the management of VMEs within national and international waters in the region. To further investigate patterns of connectivity in deep-sea squat lobster populations and provide valuable information for the design of management strategies to protect VMEs, newly developed SNPs were utilised (Chapter 5). The results showed that the Tasmanian slope and Macquarie Ridge populations were genetically different from all other populations, both within New Zealand’s exclusive economic zone (EEZ) and the high seas beyond, with little gene flow derived from Tasmanian slope populations to Macquarie Ridge populations. The results are discussed in the context of existing MPAs, and highlight the complexity of the endeavour to maintain population diversity and gene flow across multiple national jurisdictions as well as international waters, all of which employ different spatial protective measures. The findings of this research are summarised and discussed in relation to the usefulness of genetic studies to provide new and valuable information about the genetic diversity and connectivity of VME-associated species, and to highlight what additional genetic research is needed to assist in the management and conservation of VMEs in the southwest Pacific Ocean (Chapter 6).</p>

Patterns of population genetic structure and connectivity of squat lobsters associated with vulnerable marine ecosystems

<p>Vulnerable marine ecosystems (VMEs) are susceptible to the impact of intense or long-term anthropogenic activities (e.g., bottom trawling). Networks of marine protected areas (MPAs) can help facilitate the conservation and restoration of biodiversity and ecosystem function provided by VMEs. An understanding of the connectivity amongst populations of deep-sea organisms is crucial for informing the management of VMEs, by assessing the effectiveness of existing MPAs and informing the placement of new MPAs. Genetic evaluation of population structure is one of the most commonly used indirect approaches for interpreting connectivity. In contrast to corals or sponges, which are typically habitat-forming organisms as VME-indicator taxa, squat lobsters are often found in close association with VMEs and can be considered to be VME-associated taxa. Nowadays, population genetic studies of deep-sea fauna mainly focus on VME-indicator taxa, whilst relatively few studies have focussed on VME-associated taxa, such as squat lobsters, whose distribution is not exclusively limited to VMEs. In this study, three deep-sea squat lobster species, Munida isos Ahyong & Poore, 2004, Munida endeavourae Ahyong & Poore, 2004 and Munida gracilis Henderson, 1885, were selected based on their association with VMEs (e.g., cold-water coral reefs and seamounts), wide distributional ranges across the southwest Pacific Ocean, and sample availability. The overall aims of this research are to evaluate patterns of population structure and genetic connectivity of three squat lobster taxa in the southwest Pacific Ocean and consider how the acquired genetic information can contribute to the management and conservation of VMEs in the southwest Pacific Ocean. A general introduction of VMEs, MPAs, connectivity of deep-sea fauna, High-Throughput Sequencing (HTS), study area and study taxa are presented in Chapter 1. To provide background information for this research, a review was conducted of the molecular-based studies of the systematics, taxonomy and phylogenetics of marine squat lobster taxa (Chapter 2). Recent molecular-based studies have dramatically increased our understanding of squat lobster phylogenetics and systematics, and thereby the taxonomy of this diverse and challenging group, which provide a valuable starting point for evaluating hypotheses concerning speciation, biogeography, adaptation and co-evolution (e.g., squat lobsters and corals). Notably, accurate taxonomy is critical for population genetic studies and consequently supports the conservation efforts of VMEs. A range of molecular genetic markers, including the mitochondrial COI region, nuclear microsatellites and single nucleotide polymorphisms (SNPs), were utilised to evaluate the genetic connectivity amongst populations of three VME-associated taxa (Munida isos, M. endeavourae and M. gracilis). In addition to this, universal invertebrate primers were used to yield partial COI fragments of 649 bp (DNA barcoding) for the three Munida species to confirm the taxonomic identity and to exclude the possibility of cryptic species. Due to limited genetic information for the three Munida species, novel microsatellite loci were developed for M. isos based on the HiSeq 2500 sequencing platform and used for cross-species amplification in M. endeavourae and M. gracilis (Chapter 3). Additionally, a Genotyping by Sequencing (GBS) protocol and the Universal Network Enabled Analysis Kit (UNEAK) pipeline were employed to develop novel SNPs for M. isos samples from the southwest Pacific Ocean (Chapter 5). A spatially explicit hierarchical testing framework (Northern-Southern biogeographical provinces, North-Central-South regions, and individual geomorphic features) was employed for the evaluation of connectivity amongst populations of the three deep-sea squat lobster taxa across their distributional range in the southwest Pacific Ocean (Chapter 4). The level of genetic diversity was high as revealed by variation at the COI region, and moderate based on microsatellite markers across the three Munida species. With more than 96% of the variance being attributed to differences within populations in the three Munida species, based on both marker types, no genetic subdivision was detected in M. endeavourae, whilst little genetic differentiation was observed in M. isos and M. gracilis based on microsatellite variation. For M. isos, populations from the Tasmanian slope were potentially genetically different from all other populations and may act as source populations, whereas populations from the Kermadec Ridge may be sink populations. Robust evidence of recent demographic expansions was detected in the three Munida species, based on COI and microsatellite marker types. The estimated time of demographic expansions for the three Munida species was ca. 16.1 kya, 24.4 kya and 21.6 kya for the M. isos, M. endeavourae and M. gracilis, respectively, coinciding with the late Pleistocene. The results are discussed in the context of the distribution of existing MPAs, and contribute new information useful to the management of VMEs within national and international waters in the region. To further investigate patterns of connectivity in deep-sea squat lobster populations and provide valuable information for the design of management strategies to protect VMEs, newly developed SNPs were utilised (Chapter 5). The results showed that the Tasmanian slope and Macquarie Ridge populations were genetically different from all other populations, both within New Zealand’s exclusive economic zone (EEZ) and the high seas beyond, with little gene flow derived from Tasmanian slope populations to Macquarie Ridge populations. The results are discussed in the context of existing MPAs, and highlight the complexity of the endeavour to maintain population diversity and gene flow across multiple national jurisdictions as well as international waters, all of which employ different spatial protective measures. The findings of this research are summarised and discussed in relation to the usefulness of genetic studies to provide new and valuable information about the genetic diversity and connectivity of VME-associated species, and to highlight what additional genetic research is needed to assist in the management and conservation of VMEs in the southwest Pacific Ocean (Chapter 6).</p>

New species of squat lobsters of the genus Munida from Australia

This study reports on new squat lobsters of the genus Munida collected during recent surveys of Australia’s continental margins. We report on 33 species of Munida including seven new species and 14 new range extensions for Australia. More than 500 specimens were collected, mostly from the western continental margin of Australia, but also including a new species from deep water (>2000 m) off Tasmania. We provide new data on the colour patterns of some species and include molecular data from two mitochondrial markers (16S rRNA and COI) to support the taxonomic status of the new species.

Revision of the squat lobsters of the genus Phylladiorhynchus Baba, 1969 (Crustacea, Decapoda, Galatheidae) with the description of 41 new species

The genus Phylladiorhynchus Baba, 1969 currently contains 11 species, all occurring in the shallow waters and on the continental shelf of the Indian and Pacific oceans. Recent expeditions in these oceans have resulted in the collection of numerous new specimens in need of analysis. We have studied this material using an integrative approach analysing both morphological and molecular (COI and 16S) characters. We describe 41 new species and resurrect three old names: P. integrus (Benedict, 1902) and P. lenzi (Rathbun, 1907), previously synonymized with P. pusillus (Henderson, 1885), and P. serrirostris (Melin, 1939), previously synonymized with P. integrirostris (Dana, 1852). Most species of the genus are described and illustrated. Some species are barely discernible on the basis of morphological characters but are highly divergent genetically. Species of Phylladiorhynchus are mainly distinguishable by the number of epigastric spines and lateral spines of the carapace, the shape and the armature of the rostrum, the number and pattern of the ridges on the carapace and pleon, the shape of thoracic sternite 3 and the armature of the P2–4 dactyli. A dichotomous identification key to all species is provided.

Latitudinal changes in the lipid content and fatty acid profiles of juvenile female red squat lobsters (Pleuroncodes monodon) in breeding areas of the Humboldt Current System

The red squat lobster Pleuroncodes monodon is a species of high commercial value that inhabits the Humboldt Current System. Along the Chilean coast, two populations are exploited by the fishing industry, one located off the coast of Coquimbo and the other off the coast of Concepción. Yet, it is unknown whether there are differences in the “bioenergetic fuel” (measured as lipid content and fatty acid profile) of juvenile populations of these two fishing units and whether these bioenergetic compounds can be modulated by differences in the environmental parameters (such as temperature or chlorophyll-a) of their breeding areas. To shed some light on this, we measured the lipid content and fatty acid profiles of the viscera and muscle of juvenile female red squat lobsters from these two fishing units, specifically from breeding areas near long-exploited fishing grounds: a) the northern fishing unit (NFU, from 26°S to 30°S) and b) the southern fishing unit (SFU, from 32°S to 37°S). We found differences in the lipid content, fatty acid profiles, and ratios of saturated fatty acids (C16:0/C18:0) of juvenile females from these two locations. In addition, the essential fatty acids (DHA/EPA) found in the viscera versus the muscle of these lobsters varied significantly. Juvenile females from the SFU (i.e. Concepción) showed a higher lipid content compared to the juvenile females from the NFU (i.e. Coquimbo). Consistently, individuals from the SFU had a higher content of fatty acids, which also proved to be richer in saturated and monounsaturated fatty acids compared to those from the NFU. Our results are important for the fisheries in both areas because these juvenile populations are the source of new recruits for the adult populations that are exploited by the fishing industry. Our study also aids in determining which populations are healthier or of better quality in bioenergetic terms. Furthermore, increasing the incorporation of bioenergetic parameters in fishery models is essential for the recruitment and stock assessment within an ecosystem approach, since it allows for the evaluation of the nutritional condition of different fishing populations.

Squat lobsters (Crustacea: Decapoda: Anomura: Galatheoidea) from off the northwestern coast of the Baja California Peninusla, Mexico

Four species of squat lobsters were collected off the northwestern coast of the Baja California Peninsula, Mexico, during an exploratory survey of fishing resources. Janethogalathea californiensis, described from California was previously known from off the west coast of the Baja California Peninsula (two localities) and from the Gulf of California (three localities). Of the three species of Munida collected during the survey, M. tenella is recorded off the west coast of the Baja California Peninsula for the first time. These are the fourth record of M. hispida and the second record of M. quadrispina in western Mexico.

Metatranscriptomics by In Situ RNA Stabilization Directly and Comprehensively Revealed Episymbiotic Microbial Communities of Deep-Sea Squat Lobsters

ABSTRACT Shinkaia crosnieri is an invertebrate that inhabits an area around deep-sea hydrothermal vents in the Okinawa Trough in Japan by harboring episymbiotic microbes as the primary nutrition. To reveal physiology and phylogenetic composition of the active episymbiotic populations, metatranscriptomics is expected to be a powerful approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. Here, we conducted direct metatranscriptomic analysis of S. crosnieri episymbionts by applying in situ RNA stabilization equipment. As expected, we obtained RNA expression profiles that were substantially different from those obtained by conventional metatranscriptomics (i.e., stabilization after retrieval). The episymbiotic community members were dominated by three orders, namely, Thiotrichales, Methylococcales, and Campylobacterales, and the Campylobacterales members were mostly dominated by the Sulfurovum genus. At a finer phylogenetic scale, the episymbiotic communities on different host individuals shared many species, indicating that the episymbionts on each host individual are not descendants of a few founder cells but are horizontally exchanged. Furthermore, our analysis revealed the key metabolisms of the community: two carbon fixation pathways, a formaldehyde assimilation pathway, and utilization of five electron donors (sulfide, thiosulfate, sulfur, methane, and ammonia) and two electron accepters (oxygen and nitrate/nitrite). Importantly, it was suggested that Thiotrichales episymbionts can utilize intercellular sulfur globules even when sulfur compounds are not usable, possibly also in a detached and free-living state. IMPORTANCE Deep-sea hydrothermal vent ecosystems remain mysterious. To depict in detail the enigmatic life of chemosynthetic microbes, which are key primary producers in these ecosystems, metatranscriptomic analysis is expected to be a promising approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. In this study, we conducted direct metatranscriptome analysis of microbial episymbionts of deep-sea squat lobsters (Shinkaia crosnieri) by applying in situ RNA stabilization equipment. Compared to conventional metatranscriptomics (i.e., RNA stabilization after retrieval), our method provided substantially different RNA expression profiles. Moreover, we discovered that S. crosnieri and its episymbiotic microbes constitute complex and resilient ecosystems, where closely related but various episymbionts are stably maintained by horizontal exchange and partly by their sulfur storage ability for survival even when sulfur compounds are not usable, likely also in a detached and free-living state.