Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci.

In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.

Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters.

Information on the temporal stability of genetic structures is important to permit detection of changes that can constitute threats to biological resources. Large-scale harvesting operations are known to potentially alter the composition and reduce the variability of populations, and Atlantic herring (Clupea harengus) has a long history of heavy exploitation. In the Baltic Sea and Skagerrak waters, the census population sizes have declined by 35-50% over the last three decades. We compared the genetic structure of Atlantic herring in these waters sampled at least two different times between 1979 and 2003 by assaying 11 allozyme and nine microsatellite loci. We cannot detect any changes in the amount of genetic variation or spatial structure, and differentiation is weak with overall F(ST)=0.003 among localities for the older samples and F(ST)=0.002 for the newer ones. There are indications of temporal allele frequency changes, particularly in one of five sampling localities that is reflected in a relatively small local N(e) estimate of c. 400. The previously identified influence of selection at the microsatellite locus Cpa112 remains stable over the 24-year period studied here. Despite little genetic differentiation, migration among localities appears small enough to permit demographic independence between populations.

Molecular phylogeny of the model annelid Ophryotrocha.

Annelids of the genus Ophryotrocha are small opportunistic worms commonly found in polluted and nutrient-rich habitats such as harbors. Within this small group of about 40 described taxa a large variety of reproductive strategies are found, ranging from gonochoristic broadcast spawners to sequential hermaphroditic brooders. Many of the species have a short generation time and are easily maintained as laboratory cultures. Thus they have become a popular system for exploring a variety of biological questions including developmental genetics, ethology, and sexual selection. Despite considerable behavioral, reproductive, and karyological studies, a phylogenetic framework is lacking because most taxa are morphologically similar. In this study we use 16S mitochondrial gene sequence data to infer the phylogeny of Ophryotrocha strains commonly used in the laboratory. The resulting mtDNA topologies are generally well resolved and support a genetic split between hermaphroditic and gonochoristic species. Although the ancestral state could not be unambiguously identified, a change in reproductive strategy (i.e., hermaphroditism and gonochorism) occurred once within Ophryotrocha. Additionally, we show that sequential hermaphroditism evolved from a simultaneous hermaphroditic ancestor, and that characters previously used in phylogenetic reconstruction (i.e., jaw morphology and shape of egg mass) are homoplasic within the group.