Angie Díaz

An efficient method to find potentially universal population genetic markers, applied to metazoans

BackgroundDespite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families.ResultsIn order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals.ConclusionsOur new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.

Divergence time estimations and contrasting patterns of genetic diversity between Antarctic and southern South America benthic invertebrates

La diversidad, abundancia y composicion de grupos taxonomicos en el oceano Austral difiere de otros lugares del planeta debido a que su biogeografia refleja la compleja interaccion de la tectonica, oceanografia, clima y elementos biologicos desde el Eoceno. Algunos grupos de organismos marinos bentonicos muestran altos niveles de divergencia genetica entre provincias de esta region, apoyando la existencia de procesos vicariantes por tectonica de placas mientras que otros grupos, con alta capacidad dispersiva, muestran procesos de divergencia mas recientes. Mas aun, el reciente descubrimiento de larvas de decapodos no Antarticos en peninsula Antartica sugiere que algunos grupos podrian cruzar la Corriente Circumpolar Antartica. Se analizaron los niveles de divergencia genetica en especies congenericas en invertebrados bentonicos del Oceano Austral con potencial dispersivo. Para esto, se incluyo en los analisis secuencias del gen COI de un equinoideo (Sterechinus), un gastropodo (Nacella), y un bivalvo (Yoldia). Considerando los niveles de diferenciacion genetica y asumiendo la Hipotesis del Reloj Molecular, estimamos la separacion entre grupos de ambos continentes. Tambien comparamos los niveles de variacion genetica entre especies antarticas y subantarticas de Nacella y Sterechinus para determinar el efecto de los episodios glaciales del Cuaternario en su demografia. Detectamos claras diferencias geneticas entre especies congenericas antarticas y subantarticas de Sterechinus, Nacella y Yoldia. La instalacion de una barrera efectiva entre antartica y subantartica ocurrio casi al unisono (3.7 a 5.0 Ma) para estos grupos de organismos, y muy posterior a la separacion fisica de ambos continentes. Comparaciones geneticas entre especies antarticas y subantarticas detectaron menores niveles de diversidad genetica en especies antarticas sugiriendo un efecto mas pronunciado de los episodios glaciales en Antartica que en Sudamerica. Estos resultados podrian reflejar el dramatico efecto de los ciclos glaciales del Cuaternario en los tamanos poblacionales antarticos, especialmente en grupos con rangos batimetricos estrechos. El presente estudio provee nueva evidencia de los procesos de diferenciacion entre organismos antarticos y sudamericanos. Ninguno de los generos analizados mostro evidencia de flujo genico recurrente a traves de la Corriente Circumpolar Antartica desde el Mio-Plioceno. Las comparaciones geneticas indican que especies antarticas y subantarticas fueron diferencialmente afectadas por los periodos glaciales.

Antarctic shallow subtidal echinoderms: is the ecological success of broadcasters related to ice disturbance?

One characteristic pattern found in the marine Antarctic shallow environments is the unusually high proportion of species with protected and pelagic lecitotrophic development modes. However, species with planktotrophic development generally appear as the most conspicuous types of organisms in these environments. The Antarctic shallow benthos is considered as one of the most disturbed in the world, mainly due to the action of ice, thus one could hypothesize that such an environment should favor organisms with high dispersal capability. In order to test this general hypothesis, for two consecutive summers (2004–2005) and at two locations, we quantified the abundance and size distribution of most echinoderms present along bathymetric transects. Our results show the predominance of broadcasters (i.e., Sterechinus neumayeri and Odontaster validus) at a location where disturbances are common, while brooders (e.g., Abatus agassizii) only occurred at shallower depths of the least disturbed location. These results not only corroborate the hypothesis that local disturbance is an important factor generating these ecological patterns, but also suggest how ice-related disturbances could represent a major selecting agent behind the patterns of species diversity at an evolutionary scale in Antarctica.

Restricted geographic distribution and low genetic diversity of the brooding sea urchin Abatus agassizii (Spatangoidea: Schizasteridae) in the South Shetland Islands: A bridgehead population before the spread to the northern Antarctic Peninsula?

Los periodos glaciales del Pleistoceno han promovido los principales cambios climaticos del oceano Austral. Han generado el interes cientifico sobre las estrategias desarrolladas por la fauna bentonica para tolerar y superar la extension y contraccion de la capa de hielo sobre la plataforma continental. Un estudio reciente acerca de la zonacion batimetrica y distribucion de macro-invertebrados en una zona submareal somera de la Bahia Fildes (Isla Rey Jorge, islas Shetlands del Sur), resalta la presencia de una importante agregacion del erizo incubante Abatus agassizii, cuya distribucion geografica es conocida solo para localidades al sur de la convergencia antartica (Peninsula Antartica, islas Shetland del Sur e Isla Georgias del Sur en el Arco de Escocia). Sin embargo, su presencia es atipica dado a que, primero, sus poblaciones someras debieron haber sido extintas desde la vecindad de la Peninsula Antartica por los avances y retrocesos de la capa de hielo y segundo, la ausencia de estadios larvales asociado a la estrategia de incubacion como modo de desarrollo deberia limitar una recolonizacion desde areas subantarticas mas al norte. El objetivo de este estudio fue evaluar si A. agassizii puede haber sobrevivido a las glaciaciones en su estrecho rango batimetrico en las islas Shetland del Sur o ha recolonizado recientemente el area, a pesar de su baja capacidad de dispersion. A pesar de un intensivo esfuerzo de muestreo, la baja ocurrencia de A. agassizii indica que su distribucion es muy escasa a lo largo de las islas Shetland del Sur y la Peninsula Antartica y parece estar limitada a densas poblaciones someras en areas protegidas y libres del hielo en la Bahia Fildes en la Isla Rey Jorge. Ademas, estas poblaciones presentan una muy baja diversidad genetica asociada a una senal de una expansion demografica reciente. Finalmente, la reconstruccion de las relaciones filogeneticas entre las especies de Abatus, con secuencias mitocondriales del gen COI, establecieron la afinidad de la especie antartica A. agassizii con especies subantarticas. De acuerdo a los resultados obtenidos, consideramos que la presencia de esta especie en las islas Shetlands del Sur probablemente corresponde a una reciente recolonizacion desde las islas antarticas situadas mas al norte.

Mating system and evidence of multiple paternity in the Antarctic brooding sea urchin Abatus agassizii.

Broadcasting is the predominant spawning behavior among benthic marine invertebrates, mainly associated with planktotrophic and planktonic lecitotrophic development. Broadcasting allows genetic mixing that should contribute to increase the genetic diversity of a female clutch. Conversely, in brooding species characterized by protected development, oocytes are retained and only sperm is released, which is supposed to limit the number of males that contribute to a female clutch. This spermcasting behavior together with egg retention, unusually frequent among Antarctic marine invertebrates, putatively give brooders low dispersal capacities which may reduce genetic mixing and generate genetic and kinship structure at a small spatial scale. Like many other Antarctic marine benthic invertebrates, the irregular sea urchin Abatus agassizii is a spermcaster that broods its young. In this study, we assessed the genetic diversity among 66 adults using 6 polymorphic microsatellite loci and performed progeny array analyses in order to evaluate the number of mates per female as well as genetic structure at a small spatial scale. A. agassizii exhibited a polyandric system with 2–5 mates per female regardless of population density. Bayesian analyses suggested the absence of genetic structure along our 20-m transect, while relatedness among individuals did not differ from that expected under panmixia. Finally, we conclude that a limited number of males contribute to a female clutch, probably as a consequence of limited sperm dispersal and that movement of adults may be sufficient to avoid kinship structure in the population.

Genetic structure and demographic inference of the regular sea urchin Sterechinus neumayeri (Meissner, 1900) in the Southern Ocean: The role of the last glaciation

One of the most relevant characteristics of the extant Southern Ocean fauna is its resiliency to survive glacial processes of the Quaternary. These climatic events produced catastrophic habitat reductions and forced some marine benthic species to move, adapt or go extinct. The marine benthic species inhabiting the Antarctic upper continental shelf faced the Quaternary glaciations with different strategies that drastically modified population sizes and thus affected the amount and distribution of intraspecific genetic variation. Here we present new genetic information for the most conspicuous regular sea urchin of the Antarctic continental shelf, Sterechinus neumayeri. We studied the patterns of genetic diversity and structure in this broadcast-spawner across three Antarctic regions: Antarctic Peninsula, the Weddell Sea and Adélie Land in East Antarctica. Genetic analyses based on mitochondrial and nuclear markers suggested that S. neumayeri is a single genetic unit around the Antarctic continent. The species is characterized by low levels of genetic diversity and exhibits a typical star-like haplotype genealogy that supports the hypothesis of a single in situ refugium. Based on two mutation rates standardized for this genus, the Bayesian Skyline plot analyses detected a rapid demographic expansion after the Last Glacial Maximum. We propose a scenario of rapid postglacial expansion and recolonization of Antarctic shallow areas from a less ice-impacted refugium where the species survived the LGM. Considering the patterns of genetic diversity and structure recorded in the species, this refugium was probably located in East Antarctica.

The phylogenetic position and taxonomic status of Sterechinus bernasconiae Larrain, 1975 (Echinodermata, Echinoidea), an enigmatic Chilean sea urchin

Sterechinus is a very common echinoid genus in benthic communities of the Southern Ocean. It is widely distributed across the Antarctic and South Atlantic Oceans and has been the most frequently collected and intensively studied Antarctic echinoid. Despite the abundant literature devoted to Sterechinus, few studies have questioned the systematics of the genus. Sterechinus bernasconiae is the only species of Sterechinus reported from the Pacific Ocean and is only known from the few specimens of the original material. Based on new material collected during the oceanographic cruise INSPIRE on board the R/V Melville, the taxonomy and phylogenetic position of the species are revised. Molecular and morphological analyses show that S. bernasconiae is a subjective junior synonym of Gracilechinus multidentatus (Clark). Results also show the existence of two genetically distinct subclades within the so-called Sterechinus clade: a Sterechinus neumayeri subclade and a subclade composed of other Sterechinus species. The three nominal species Sterechinus antarcticus, Sterechinus diadema, and Sterechinus agassizi cluster together and cannot be distinguished. The species Sterechinus dentifer is weakly differentiated from these three nominal species. The elucidation of phylogenetic relationships between G. multidentatus and species of Sterechinus also allows for clarification of respective biogeographic distributions and emphasizes the putative role played by biotic exclusion in the spatial distribution of species.