Jose L. Horreo

Molecular Organization and Evolution of 5S rDNA in the Genus Merluccius and Their Phylogenetic Implications

The molecular organization of the 5S rRNA gene family has been studied in a wide variety of animal taxa, including many bony fish species. It is arranged in tandemly repeated units consisting of a highly conserved 120 base pair–long region, which encodes for the 5S rRNA, and a nontranscribed spacer (NTS) of variable length, which contains regulatory elements for the transcription of the coding sequence. In this work, a comparative analysis of 5S ribosomal DNA (rDNA) organization and evolution in the 12 species of the genus Merluccius, which are distributed in the Atlantic and Pacific oceans, was carried out. Two main types of 5S rDNA (types A and M) were identified, as differentiated by the absence or presence of a simple sequence repeat within the NTS. Four species exhibited the 2 types of 5S rDNA, whereas the rest showed only 1 type. In addition, the species M. albidus and M. bilinearis showed 2 variants (S and L) of type-M 5S rDNA, which differentiated by length. The results obtained here support the hypothesis of a 5S rRNA dual system as an ancient condition of the Piscine genome. In contrast, some inconsistencies were found between the phylogeny of the genus Merluccius based on mitochondrial genes and that obtained from nuclear markers (5S rDNA, microsatellite loci, and allozyme data). Hybrid origin of the American species M. australis is suggested based on these results.

Universal primers for species authentication of animal foodstuff in a single polymerase chain reaction

BACKGROUND There are many DNA-based systems for detecting animal species present in food and food products, applicable for food quality control and authentication. However, most (if not all) methods require more than one pair of primers and cannot be applied over a wide taxonomic range, e.g. identifying vertebrates and invertebrates with the same primers and protocols. RESULTS A pair of primers is described here that allows in a single polymerase chain reaction the identification of animal species in food and processed (precooked, canned or smoked) food products over a wide taxonomic range. CONCLUSION These primers permit the identification of most animal taxa employed in human nutrition, from invertebrates such as molluscs to higher vertebrates, distinguishing between species of the same genus. The short fragment amplified within the 16S rDNA exhibits phylogenetic value and could be considered universal based on the wide taxonomic range assayed. The primers are easy to use and accessible for laboratories with a modest budget, as well as being valuable for consumer information and to reveal food fraud.

Mislabeling of Two Commercial North American Hake Species Suggests Underreported Exploitation of Offshore Hake

Abstract Mislabeling of North American merlucciid hakes in stock surveys and commercial market samples was detected by employing nuclear 5S ribosomal DNA (rDNA) and mitochondrial cytochrome b variation as molecular markers. Results showed that offshore hake Merluccius albidus is sold in European markets but is labeled as the morphologically similar silver hake M. bilinearis, which is the target species of the fishery. This suggests that offshore hake may be inadvertently included within silver hake landings, as the two species overlap in the southern area of silver hake distribution (approximately 41°-35°N latitude near North American coasts). An inexpensive and technically easy technique based on polymerase chain reaction (PCR) amplification of a fragment of 5S rDNA and visualization of PCR products in agarose gels is recommended for routine species assignation in landings for purposes of exploitation estimates and for authentication of commercial hake species.

Same old Salmo? Changes in life history and demographic trends of North Iberian salmonids since the Upper Palaeolithic as revealed by archaeological remains and beast analyses

Life history traits determine fitness and hence the ability of populations and species to survive through adverse conditions. Therefore, identifying temporal changes in life history traits over large timescales is necessary to understand and predict the effect of current global change on wild populations. In this study, we compare life history traits between Palaeolithic and present‐day vertebrates, analysing the number of winters spent in the river and at sea by North Iberian salmonids (Salmo salar and Salmo trutta) from two separate time frames: the Upper Palaeolithic, based on archaeological remains, and the present day, based on sport catches. The river stage did not change significantly, but the marine period has been shortened in modern anadromous specimens, accordingly shortening mean generation time. Population growth rates have been estimated through Bayesian analyses of the mitochondrial DNA control region of modern specimens for the two Salmo species using two different mutation rates (1% and 3.6%). Coincidence of coalescent Ne estimates with independent Ne calculated from catches suggests that the 3.6% mutation rate fits better the evolution of the studied populations. Population growth rate declines would have occurred in the last millennium and could be explained by a combination of climatic events and anthropogenic activities.

Atlantic Salmon at Risk: Apparent Rapid Declines in Effective Population Size in Southern European Populations

Abstract Populations of southern European Atlantic salmon Salmo salar are subjected to exploitation by sportfishing and exhibit evidence of dramatic catch reduction for the same fishing effort over recent history. We employed nine microsatellite loci as markers to estimate effective population sizes of Atlantic salmon in five rivers of northern Spain for comparison with 1990s data describing the same populations; marked declines in effective population sizes over the last decade were detected, and a reduced census size is proposed to be one of the probable causes. These estimates highlight the endangered status of the Atlantic salmon populations in northern Spain. A reduction in fishing effort and an increase in protective measures are recommended for the conservation of these fragile populations at the southernmost edge of the species’ natural distribution.

Geography and major host evolutionary transitions shape the resource use of plant parasites

Significance Patterns of host use by parasites are commonly thought to be limited by phylogenetic constraints, yet little is known about the role of the geographic distribution of hosts and parasites in such patterns. We show that evolutionary patterns in host use by a family of plant parasites are largely determined by the geographical distribution of hosts and parasites. Such phylogenetic lability in host use results in repeated colonizations of distantly related plant lineages, even across major plant evolutionary transitions. Still, these transitions constitute significant adaptive barriers in the evolution of host use. Our results thus show that host plant use by parasitic mites hinges more on where the plant and the mite are than on phylogenetic constraints. The evolution of resource use in herbivores has been conceptualized as an analog of the theory of island biogeography, assuming that plant species are islands separated by phylogenetic distances. Despite its usefulness, this analogy has paradoxically led to neglecting real biogeographical processes in the study of macroevolutionary patterns of herbivore–plant interactions. Here we show that host use is mostly determined by the geographical cooccurrence of hosts and parasites in spider mites (Tetranychidae), a globally distributed group of plant parasites. Strikingly, geography accounts for most of the phylogenetic signal in host use by these parasites. Beyond geography, only evolutionary transitions among major plant lineages (i.e., gymnosperms, commelinids, and eudicots) shape resource use patterns in these herbivores. Still, even these barriers have been repeatedly overcome in evolutionary time, resulting in phylogenetically diverse parasite communities feeding on similar hosts. Therefore, our results imply that patterns of apparent evolutionary conservatism may largely be a byproduct of the geographic cooccurrence of hosts and parasites.

Interspecific hybridization, a matter of pioneering? Insights from Atlantic salmon and brown trout.

Interspecific hybridization may occur in situations of recent contact between a colonizer and a resident species, being more intense in the colonization front. Atlantic salmon Salmo salar and brown trout S. trutta have been sympatric species since their origin and they share spatial and temporal spawning niches, exhibiting low levels of bidirectional interspecific hybridization and introgression throughout their distribution range. Different causes have been identified for increased hybridization, from escapes or deliberate releases of domesticated fish to sneaking male behavior. We have examined hybridization rates and direction in different situations of advance of one of these species into a territory formerly inhabited by the other (247 samples were analyzed in northern Spain and 487 in Kerguelen Islands). In all cases, hybrids found in the colonization front were offspring of colonizer females and resident males. We hypothesize that these findings are the result of adaptive relaxed mate choice of colonizing females, regardless of the relative abundance of each species.

CHRONOLOGICAL CHANGES IN UPPER PALEOLITHIC FISHERIES REVEALED BY MUSEUM ARCHIVAL MATERIAL

ABSTRACT Salmonid vertebrae in mixed faunal remains from North Iberian archaeological sites of the upper Paleolithic were analyzed to determine specimen age, migratory status, and the seasonality of catch, based on annual growth marks. Fish size was back calculated from vertebra size using published equations. Although sample size is very small, significant changes in the average size and migratory status of fished specimens, and in the seasonality of fishing were detected. Salmonids (Atlantic salmon Salmo salar and brown trout Salmo trutta) were present as a resource in human diet in different climatic conditions. However, preferential winter harvest was prevalent starting after the Last Glacial Maximum, although this may be an artifact of the data related to sea-level rise. The main potential impact of prehistoric fishing habits on salmonid populations was the removal of the larger breeders from the rivers, thus indirectly promoting the reproduction of smaller fish (i.e., selection for small size, although most likely unintended). The methodology described in this study, if applied to larger collections and/or samples, can provide information on how salmonids reacted to past changes in harvest or climate, and could help to predict the consequences of current environmental and climatic changes.

The Meeting of Waters, a possible shelter of evolutionary significant units for Amazonian fish

Identification of priority conservation areas is crucial for safeguarding freshwater ecosystems. Occurrence of unique populations and/or evolutionary significant units for key species is one of the most frequent reasons for protecting a region or location. In this study we have studied two of the most important fisheries resources of the Amazon basin, Curimata and Tambaqui, from different areas, in order to identify common zones of special diversity. Employing the Barcoding cytochrome oxidase I gene as a genetic tool, we have detected a clear differentiation of the populations inhabiting the Meeting of Waters and the rest of the basin for both species. This area corresponds to the confluence of the Solimões and the Negro rivers, of different physicochemical water characteristics, at the Brazilian city of Manaus in central Amazonas. The Meeting of Waters area (near Manaus) could be recommended as a potential area subject of special management, given its apparent role as a shelter for evolutionary significant units.

Nature versus nurture? Consequences of short captivity in early stages

Abstract Biological changes occurring as a consequence of domestication and/or captivity are not still deeply known. In Atlantic salmon (Salmo salar), endangered (Southern Europe) populations are enhanced by supportive breeding, which involves only 6 months of captive rearing following artificial spawning of wild‐collected adults. In this work, we assess whether several fitness‐correlated life‐history traits (migratory behavior, straying rate, age at maturity, and growth) are affected by early exposure to the captive environment within a generation, before reproduction thus before genetic selection. Results showed significant differences in growth and migratory behavior (including straying), associated with this very short period of captivity in natural fish populations, changing even genetic variability (decreased in hatchery‐reared adults) and the native population structure within and between rivers of the species. These changes appeared within a single generation, suggesting very short time of captivity is enough for initiating changes normally attributed to domestication. These results may have potential implications for the long‐term population stability/viability of species subjected to restoration and enhancement processes and could be also considered for the management of zoo populations.