Insights into the Migration Routes and Historical Dispersion of Species Surviving the Messinian Crisis: The Case of Patella ulyssiponensis and Epizoic Rhodolith Lithophyllum hibernicum

The genus Patella (Patellogastropoda, Mollusca) is represented by a group of species exclusive to the Northeast Atlantic Ocean (including Macaronesian archipelagos) and Mediterranean Sea. The species Patella ulyssiponensis and Patella aspera are common in European waters, with the first inhabiting continental coast, and the second endemic to Macaronesian archipelagos. However, the acceptance of these two lineages as separate species is still highly debated. The red coralline species algae Lithophyllum hibernicum, distributed from Northeast Atlantic to the Mediterranean, is usually found as epilithic crusts or unattached forms (named rhodolith beds), although it also forms epizoic crusts on other organisms, e.g., shell surfaces. In order to study the historic dispersal and migration routes of the Patella ulyssiponensis-aspera complex, taxonomic, genetic and biogeographic approaches were employed based on haplotype network analyses and estimations for the most common recent ancestor (TMRCA), using Cytochrome Oxydase I. A synonymy for these two species is proposed, with the presence of a shared haplotype between the continental (P. ulyssiponensis) and insular (P. aspera) lineages, and with basis of morphological and nomenclatural data. We propose an evolutionary scenario for its dispersal based on a high haplotype diversity for the Mediterranean regions, indicating its possible survival during the Messinian Salinity Crisis (6–5.3 Mya), followed by a colonization of the Proto-Macaronesian archipelagos. The epizoic association of L. hibernicum on P. ulyssiponensis shell adult surface is recorded in this study, likewise the promotion of settlement conditions provided by these coralline algae to P. ulyssiponensis larvae, may explain the reach of P. ulyssiponensis distribution through rhodolith transportation.

Population Genetics of the Teleost Orange Roughy, Hoplostethus Atlanticus, and Insights into their Visual Adaptations to the Deep-Sea Environment

<p>The orange roughy, Hoplostethus atlanticus, has been one of the main targeted species in deep-sea fisheries worldwide. It occurs at depths of 450 – 1800 m and is abundant off the coasts of New Zealand, Australia, Namibia, Chile, and in the Northeast Atlantic Ocean. Like many other deep-sea fishes, orange roughy is vulnerable to over exploitation because they grow slow reaching maturity at about 30 years and live for more than 100 years. Their fecundity is low, which means they have low productivity. The individuals form predictable and dense spawning aggregations close to seamounts, plateaus and canyons. The trawl fishery for orange roughy started in seamounts around New Zealand in the late 1970s and progressively expanded off the coast of other countries and to the high seas (out of any Economic Exclusive Zone). Most stocks have been fished down to or below 30% pre-exploitation levels; as a consequence, fisheries have been closed or catches largely reduced. Currently, the only large scale fisheries operate off New Zealand. For effective fisheries management it is essential to define real biological units or “stocks”. There has been considerable research into the levels of population differentiation of orange roughy using a range of techniques at different geographic scales to attempt to differentiated stocks. However, there is no consensus about the level of connectivity among populations. In the present study, I investigated the levels of population differentiation in orange roughy using two types of neutral molecular markers at a global and fine-scales. Both markers revealed high levels of genetic diversity which is likely related with historically large population sizes. The analyses of 546 cytochrome c oxidase subunit I (COI) sequences revealed a lack of global genetic differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation was found between the Southern hemisphere sites and two Northeast Atlantic sites. Mismatch distribution and Bayesian analyses indicated the occurrence of expansion events in orange roughy during the Pleistocene period. A data set of nine microsatellite DNA loci genotyped from 812 individuals, showed a predominant lack of significant genetic differentiation across the Tasman Sea and at a fine-scale around New Zealand. At a global scale, differentiation was low but significant across the Southern hemisphere; and the highest values of differentiation were detected between the Southern hemisphere sites and the Northeast Atlantic Ocean. The predominant lack of differentiation at the regional and fine-scale and the low differentiation within the Southern hemisphere is probably the result of stepping-stone dispersal of long-lived adults that are able to spawn many times in their life. Most orange roughy studies have been oriented to fisheries aspects, but other kind of studies as the genetic divergence and phylogenetic relationships among Hoplostethus species are lacking. Using available COI sequences, I conducted a phylogenetic study including H. atlanticus, H. crassispinus, H. gigas, H. japonicus H. latus, and H. mediterraneus. As expected, the inter species divergence was much higher than the intra species divergence. Phylogenetics analyses showed that H. latus, H. crassispinus, H. japonicus, and H. mediterraneus form a separate clade from H. atlanticus and H. gigas. The position of H. gigas was not well defined with the nucleotide data. However, at the amino acid level, non-synonymous substitutions differentiated H. atlanticus from all the other species. This was correlated with morphological characteristics presented elsewhere. A candidate gene approach was attemped using the rhodopsin gene; however, there was almost no variation among partial sequences of individuals from distant sites. Instead, this gene was used to investigate the molecular basis for visual adaptations in orange roughy to the bathypelagic light environment. It is known that certain amino acid replacements in the rhodopsin gene of vertebrates shift the λmax value of the pigment to perceive different light conditions. To compare and identify critical amino acid sites that are known to be involved in spectral tuning, I obtained partial rhodopsin sequences of other 18 marine teleost habiting at different depths (1 – 1,175 m) and, thus, different light environments. A phylogenetic analysis was conducted to determine whether particular rhodopsin gene sequences correlate with the depths occupied by the species. I identified four critical amino acid replacements that have been involved in the spectral tuning of rod pigments. Orange roughy presented the same amino acid combination at two critical sites already reported for the deep-sea congener silver roughy, which was not found in any of the other species. This likely reflects an adaptation to the light available (i.e. bioluminescence) in the bathypelagic environment. The phylogeny was weakly related to the maximum depth of the species, probably because there are selectively neutral (i.e. inherited by ancestry) and non-neutral changes (i.e. influenced by natural selection) among the rhodopsin sequences of the species being considered.</p>

Population Genetics of the Teleost Orange Roughy, Hoplostethus Atlanticus, and Insights into their Visual Adaptations to the Deep-Sea Environment

<p>The orange roughy, Hoplostethus atlanticus, has been one of the main targeted species in deep-sea fisheries worldwide. It occurs at depths of 450 – 1800 m and is abundant off the coasts of New Zealand, Australia, Namibia, Chile, and in the Northeast Atlantic Ocean. Like many other deep-sea fishes, orange roughy is vulnerable to over exploitation because they grow slow reaching maturity at about 30 years and live for more than 100 years. Their fecundity is low, which means they have low productivity. The individuals form predictable and dense spawning aggregations close to seamounts, plateaus and canyons. The trawl fishery for orange roughy started in seamounts around New Zealand in the late 1970s and progressively expanded off the coast of other countries and to the high seas (out of any Economic Exclusive Zone). Most stocks have been fished down to or below 30% pre-exploitation levels; as a consequence, fisheries have been closed or catches largely reduced. Currently, the only large scale fisheries operate off New Zealand. For effective fisheries management it is essential to define real biological units or “stocks”. There has been considerable research into the levels of population differentiation of orange roughy using a range of techniques at different geographic scales to attempt to differentiated stocks. However, there is no consensus about the level of connectivity among populations. In the present study, I investigated the levels of population differentiation in orange roughy using two types of neutral molecular markers at a global and fine-scales. Both markers revealed high levels of genetic diversity which is likely related with historically large population sizes. The analyses of 546 cytochrome c oxidase subunit I (COI) sequences revealed a lack of global genetic differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation was found between the Southern hemisphere sites and two Northeast Atlantic sites. Mismatch distribution and Bayesian analyses indicated the occurrence of expansion events in orange roughy during the Pleistocene period. A data set of nine microsatellite DNA loci genotyped from 812 individuals, showed a predominant lack of significant genetic differentiation across the Tasman Sea and at a fine-scale around New Zealand. At a global scale, differentiation was low but significant across the Southern hemisphere; and the highest values of differentiation were detected between the Southern hemisphere sites and the Northeast Atlantic Ocean. The predominant lack of differentiation at the regional and fine-scale and the low differentiation within the Southern hemisphere is probably the result of stepping-stone dispersal of long-lived adults that are able to spawn many times in their life. Most orange roughy studies have been oriented to fisheries aspects, but other kind of studies as the genetic divergence and phylogenetic relationships among Hoplostethus species are lacking. Using available COI sequences, I conducted a phylogenetic study including H. atlanticus, H. crassispinus, H. gigas, H. japonicus H. latus, and H. mediterraneus. As expected, the inter species divergence was much higher than the intra species divergence. Phylogenetics analyses showed that H. latus, H. crassispinus, H. japonicus, and H. mediterraneus form a separate clade from H. atlanticus and H. gigas. The position of H. gigas was not well defined with the nucleotide data. However, at the amino acid level, non-synonymous substitutions differentiated H. atlanticus from all the other species. This was correlated with morphological characteristics presented elsewhere. A candidate gene approach was attemped using the rhodopsin gene; however, there was almost no variation among partial sequences of individuals from distant sites. Instead, this gene was used to investigate the molecular basis for visual adaptations in orange roughy to the bathypelagic light environment. It is known that certain amino acid replacements in the rhodopsin gene of vertebrates shift the λmax value of the pigment to perceive different light conditions. To compare and identify critical amino acid sites that are known to be involved in spectral tuning, I obtained partial rhodopsin sequences of other 18 marine teleost habiting at different depths (1 – 1,175 m) and, thus, different light environments. A phylogenetic analysis was conducted to determine whether particular rhodopsin gene sequences correlate with the depths occupied by the species. I identified four critical amino acid replacements that have been involved in the spectral tuning of rod pigments. Orange roughy presented the same amino acid combination at two critical sites already reported for the deep-sea congener silver roughy, which was not found in any of the other species. This likely reflects an adaptation to the light available (i.e. bioluminescence) in the bathypelagic environment. The phylogeny was weakly related to the maximum depth of the species, probably because there are selectively neutral (i.e. inherited by ancestry) and non-neutral changes (i.e. influenced by natural selection) among the rhodopsin sequences of the species being considered.</p>

First thorough assessment of de novo oocyte recruitment in a teleost serial spawner, the Northeast Atlantic mackerel (Scomber scombrus) case

The understanding of teleost fecundity type (determinate or indeterminate) is essential when deciding which egg production method should be applied to ultimately estimate spawning stock biomass. The fecundity type is, however, unknown or controversial for several commercial stocks, including the Northeast Atlantic mackerel (Scomber scombrus). Aiming at solving this problem, we applied state-of-the-art laboratory methods to document the mackerel fecundity type, including any de novo oocyte recruitment during spawning. Initially, active mackerel spawning females were precisely classified according to their spawning status. The number and size of all phasei-specific oocytes (12 phases), with a special attention to previtellogenic oocytes phases (PVO [PVO2 to PVO4a–c]), were also thoroughly investigated. Examinations of relative fecundity (RFi) clarified that the latest phase of PVOs (PVO4c) are de novo recruited to the cortical alveoli–vitellogenic pool during the spawning period, resulting in a dome-shaped seasonal pattern in RFi. Hence, we unequivocally classify mackerel as a true indeterminate spawner. As PVO4c oocytes were currently identified around 230 µm, mackerel fecundity counts should rather use this diameter as the lower threshold instead of historically 185 µm. Any use of a too low threshold value in this context will inevitably lead to an overestimation of RFi and thereby underestimated spawning stock biomass.