Isolation mediates persistent founder effects on zooplankton colonisation in new temporary ponds

Understanding the colonisation process in zooplankton is crucial for successful restoration of aquatic ecosystems. Here, we analyzed the clonal and genetic structure of the cyclical parthenogenetic rotifer Brachionus plicatilis by following populations established in new temporary ponds during the first three hydroperiods. Rotifer populations established rapidly after first flooding, although colonisation was ongoing throughout the study. Multilocus genotypes from 7 microsatellite loci suggested that most populations (10 of 14) were founded by few clones. The exception was one of the four populations that persisted throughout the studied hydroperiods, where high genetic diversity in the first hydroperiod suggested colonisation from a historical egg bank and, no increase in allelic diversity was detected with time. In contrast, in another of these four populations, we observed a progressive increase of allelic diversity. This population became less differentiated from the other populations suggesting effective gene flow soon after its foundation. Allelic diversity and richness remained low in the remaining two, more isolated, populations, suggesting little gene flow. Our results highlight the complexity of colonisation dynamics, with evidence for persistent founder effects in some ponds, but not in others, and with early immigration both from external source populations, and from residual, historical diapausing egg banks

Colonization and dispersal patterns of the invasive American brine shrimp Artemia franciscana (Branchiopoda: Anostraca) in the Mediterranean region

Cysts of the brine shrimp Artemia franciscana are harvested from the Great Salt Lake (GSL) and San Francisco Bay (SFB) saltworks in the USA, and marketed worldwide to provide live food for aquaculture. This species has become invasive across several countries. We investigated (1) if the introduced populations in the Mediterranean region could have originated from these USA populations, (2) how the genetic diversity of Mediterranean compares to that at GSL and SFB, and (3) if genetic patterns in the Mediterranean can shed light on colonization routes. We sequenced a fragment of the cytochrome c oxidase subunit I and screened microsatellites loci from Mediterranean populations and the two putative USA sources. Haplotypes from Mediterranean populations were identical or closely related to those from SFB and GSL, and not related to other available American populations. Microsatellite analyses showed a reduced population diversity for most Mediterranean populations suggesting bottleneck effects, but few populations were showing similar or higher genetic diversity than native ones, which are likely to be admixed from both GSL and SFB because of multiple introductions. Results suggest natural dispersal, potentially via flamingos, between two Spanish populations. Our analyses show that all invaded populations could have originated from those commercialized USA populations. © 2013 Springer Science+Business Media Dordrecht

Cross-species tests of 45 microsatellite loci isolated from different species of ungulates in the Iberian red deer (Cervus elaphus hispanicus) to generate a multiplex panel

The Iberian red deer (Cervus elaphus hispanicus) is an emblematic game species in Spain. To generate a battery of polymorphic markers for multiplex polymerase chain reactions for the Spanish red deer, 45 loci isolated in different species of ungulates were tested. Of the primers tested, 27 amplified but only 21 were polymorphic. Eleven of these markers were subsequently optimized for multiplex in four polymerase chain reactions. This allows analysing several molecular markers jointly to substantially reduce costs. Finally, we report descriptive summary statistics such as number of alleles for the former and also test of disequilibria and heterozygosity for the latter. © 2008 The Authors.Peer Reviewe

Species identification and morphological differences of anguillid glass eels recruiting to Viti Levu Island of Fiji in the western South Pacific

There are six species of anguillid eels that live in various regions of the western South Pacific but the species compositions of glass eels recruiting to many of the islands of the region are not well known. A total of 1368 anguillid glass eels were collected fortnightly at the mouth of a small river at Namelimeli near Navua in Fiji Islands between April 2015 and June 2016. These were found through DNA barcoding to have a species composition comprising of two longfin eels Anguilla marmorata and A. megastoma, and one shortfin eel A. obscura. 35 glass eels from each species were then selected for morphological studies, it was found that the external morphological characters of anodorsal length ratios, caudal pigmentation patterns, and the internal characters of total, predorsal, and anodorsal vertebral counts were sufficient to classify these three species using morphological characters alone. These findings will simplify research and monitoring techniques of anguillid glass eel recruitment for conservation, fisheries management or aquaculture purposes in the South Pacific

Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis

Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e., heterochiasmy), which is also poorly understood. The family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have nonhomologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species and four genera). Although nonhomology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify quantitative trait loci (QTL) for 21 unique growth, reproductive, and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution

Estimación de la diversidad genética y del tamaño efectivo de la población de coquina Donax trunculus del Parque Nacional de Doñana y su contribución a áreas no protegidas

Este capítulo contiene 16 páginas, 4 tablas, 6 figuras.[EN]We have studied seven populations of the wedge clam Donax trunculus, distributed throught the Spanish Atlantic and Mediterranean coasts. A comparative analysis of size and density was performed from a sample obtained from a commercially exploited population from Isla Canela, and from another population which is managed under a strict plan using only artisanal hand dredging from the beach of the Doñana National Park showing that the management carried out in the Doñana National Park is correct and allows sustainable fisheries. Twenty one microsatellite loci were isolated and characterized in D. trunculus of which 16 were polymorphic and codominant. At least 12 of them have high frequencies of null alleles in all populations, and the rest in most populations. All collected samples were genotyped with these 16 loci and genetic diversity indices, tests of disequiibrium, fixation indices and probabilities of genetic differentiation among localities were determined. The odds of assignment to the sampling location were also determined. Several analyses were conducted to determine the potential causes for the deviations from Hardy-Weinberg equilibrium which shown that they were mainly due to the presence of null alleles. Furthermore, using the ribosomal internal transcribed spacer it was determined that the commercially exploited populations of the wedge clam under the specific name Donax trunculus are actually a mixture of a hybrid and non-hybrid species. The analysis of the genetic structure made both to all individuals and separately for hybrid and non-hybrid individuals showed four genetically distinct populations in the Spanish coast. The first in the Cantabric Sea, the second in the Gulf of Cadiz, the third from the Strait of Gibraltar to Cabo de Gata and the last one from the Cabo de Gata to the Gulf of Rosas.[ES]Se han estudiado ejemplares de coquina, Donax trunculus en 7 localidades distribuidas por las costas peninsulares atlánticas y mediterráneas españolas. Se ha hecho un análisis comparado de datos de tallas y densidad obtenidos en una localidad explotada (Isla Canela) y otra protegida (playa del Parque Nacional de Doñana), que muestran que la gestión llevada a cabo en el Parque Nacional Doñana es la correcta y permite una pesca sostenible. Se aislaron y caracterizaron 21 loci de microsatélites de los cuales 16 resultaron polimórficos y codominantes. De ellos al menos 12 presentan elevadas frecuencias de alelos nulos en todas las poblaciones, y el resto en la mayoría de poblaciones. Todas las muestras fueron genotipadas con estos 16 loci y se determinaron los índices de diversidad genética, pruebas de equilibrio, índices de fijación y las probabilidades de diferenciación entre localidades. También se determinaron las probabilidades de asignación a la localidad de muestreo. Se realizaron diversos análisis para determinar las causas potenciales de las desviaciones del equilibrio de Hardy-Weinberg y se demostró que se deben principalmente a alelos nulos. Se descubrió mediante el análisis del marcador ribosomal ITS que las poblaciones de coquina explotadas comercialmente en España bajo la denominación específica Donax trunculus son en realidad una mezcla de una especie híbrida y una no híbrida. El análisis de la estructura genética, tanto el realizado a todos los individuos como de forma separada para individuos híbridos y no-híbridos, demostró que existen cuatro poblaciones genéticamente distintas en el litoral español. La primera en el Mar Cantábrico, la segunda en el Golfo de Cádiz, la tercera entre el Estrecho de Gibraltar y el Cabo de Gata y la última entre el Cabo de Gata y el Golfo de Rosas.Queremos agradecer en primer lugar al Organismo Autónomo Parques Nacionales por la concesión del proyecto que permitió el presente estudio. A la oficina de coordinación del Parque Nacional de Doñana por las facilidades prestadas para los muestreos en la playa de Doñana. Nuestro agradecimiento también a Consejería de Agricultura, Pesca y Desarrollo Rural de la Junta de Andalucía por compartir sus datos sobre la densidad de coquinas en el Golfo de Cádiz y facilitar los permisos de pesca en los diferentes puntos de Andalucía. Y como no, gracias también a los mariscadores y pescadores de Sanlú- car de Barrameda (Cádiz) y de Cabo de Gata (Almería) que nos acompañaron en los diferentes muestreos.Peer reviewe

Kinship genomics approach to study mating systems in a depleted sea turtle rookery

Knowledge of demographic processes and life history strategies is necessary for the conservation and management of endangered sea turtle populations, but it is difficult to ascertain because of the limited accessibility to marine environments that sea turtles use during the different stages of their life cycle. In such cases, molecular genetics and genomic approaches are useful to assess mating systems and operational sex ratios (OSR), which ultimately influence demography. This pilot study used genome-wide single nucleotide polymorphism (SNP) genetic markers for exploring kinship and mating systems in sea turtles where major obstacles prevent a comprehensive assessment in the wild. We sampled 217 young hawksbill turtles (Eretmochelys imbricata) of unknown parentage that had originally been collected locally from seven nests and were being temporarily kept in captivity by Treasure Island Ltd as part of its captive rearing conservation project at Bounty and Treasure Islands, Fiji, in the South Pacific. The raw dataset comprised 13,573 SNPs, of which we retained 639 SNPs for parentage and relatedness analyses. Our findings from seven different pairs of parents suggest a 1:1 male:female OSR and demonstrate that genome-wide SNP genotyping approaches can be used to infer OSR. Knowledge of OSR can help evaluate the magnitude of the impact of warming temperatures and consequent feminisation in sea turtles. Our approach can complement or substitute field observation of breeding males and nesting females when logistical or budgetary constraints prevent observation of OSR in wild sea turtle populations. This approach allows inference of OSR. Protection of beaches with a higher number of pairs of parents should be prioritised to increase genetic resilience. Conservation actions in rookeries with a female-skewed OSR should be prioritised to address population declines in the long run

The role of humans in the diversification of a threatened island raptor

<p>Abstract</p> <p>Background</p> <p>Anthropogenic habitat modifications have led to the extinction of many species and have favoured the expansion of others. Nonetheless, the possible role of humans as a diversifying force in vertebrate evolution has rarely been considered, especially for species with long generation times. We examine the influence that humans have had on the colonization and phenotypic and genetic differentiation of an insular population of a long-lived raptor species, the Egyptian vulture (<it>Neophron percnopterus</it>).</p> <p>Results</p> <p>The morphological comparison between the Canarian Egyptian vultures and the main and closest population in Western Europe (Iberia) indicated that insular vultures are significantly heavier (16%) and larger (about 3%) than those from Iberia. Bayesian and standard genetic analyses also showed differentiation (<it>F<smcaps>_ST</smcaps></it>= 0.11, <it>p </it>< 0.01). The inference of changes in the effective size of the Canarian deme, using two likelihood-based Bayesian approaches, suggested that the establishment of this insular population took place some 2500 years ago, matching the date of human colonization. This is consistent with the lack of earlier fossils.</p> <p>Conclusions</p> <p>Archaeological remains show that first colonizers were Berber people from northern Africa who imported goats. This new and abundant food source could have allowed vultures to colonize, expand and adapt to the island environment. Our results suggest that anthropogenic environmental change can induce diversification and that this process may take place on an ecological time scale (less than 200 generations), even in the case of a long-lived species.</p

Isolation and characterization of polymorphic microsatellite markers for peacock wrasse (Symphodus tinca)

Eight polymorphic microsatellite loci were isolated and characterized for the peacock wrasse (Symphodus tinca), a labrid fish inhabiting the Mediterranean and Black seas. Characterization of 35 individuals from the western Mediterranean indicated a relatively high allelic diversity (mean = 12.4, range 9-17), and observed heterozygosity ranging from 0.65 to 0.91. We found no evidence of linkage disequilibrium between pairs of loci. Two loci showed significant departure from Hardy-Weinberg equilibrium. These polymorphic markers can be useful in most basic population genetic applications. © 2006 The Authors.Peer Reviewe

Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations