The northern gene flow into southeastern East Asians inferred from genome-wide array genotyping

The population history of Southeast China remains poorly understood due to the sparse sampling of present-day populations and far less modeling with ancient genomic data. We here newly reported genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien-speaking She people from Fujian and Taiwan, southeast China. We co-analyzed with 66 early-Neolithic to Iron-Age ancient Fujian and Taiwan individuals obtained from literature to explore the genetic continuity and admixture based on the genetic variations of high-resolution time transect. We found the genetic differentiation between northern and southern East Asians defined by a north-south East Asian genetic cline and the studied southern East Asians were clustered in the southern end of this cline. We also found that southeastern coastal continental modern East Asians harbored the genetic differentiation with other southern Tai-Kadai, Hmong-Mien, Austronesian and Austroasiatic speakers, as well as geographically close Neolithic-to-Iron Age populations, but relatedly close to post-Neolithic Yellow River ancients, which suggested the influence of southward gene flow on the modern southern coastal gene pool. Besides, we also identified one new Hmong-Mien genetic cline in East Asia with the coastal Fujian She localizing at the intersection position between Hmong-Mien and Han clines in the principal component analysis. She people show stronger genetic affinity with southern East Asian indigenous populations with the main ancestry deriving from Hanben-related populations. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to southeastern ancient indigenous rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Interestingly, f4-statistics and three-way admixture model results showed both coastal ancient sources related to Austronesian speakers and inland ancient sources related to Austroasiatic speakers complexed the modern observed fine-scale genetic structure here. Our estimated north-south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in Southeast Asia.

The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic

Coastal Atlantic cod (Gadus morhua) in the Northeast Atlantic has seen a continuous decline since the industrialization of the coastal fishery and management needs to address the spatial and temporal complexities of coexisting cod stocks. Toward that end, genetic analyses and oceanographic modelling of coastal and oceanic cod larval drift patterns were combined to elucidate the mechanisms responsible for an observed genetic cline over a >1500 km stretch along the coast of Norway. The results indicate that the north-south cline in coastal cod represents an extended contact zone between genetically divergent North Sea and North East Arctic cod and is maintained by two-way gene flow: by northward drift of pelagic eggs and larvae and by southward spawning migrations of North East Arctic cod. Computer simulations verify that the genetic cline can be established rapidly if gene flow into coastal populations is substantial. The shape of the cline, on the other hand, was found to be largely insensitive to the total amount of gene flow and therefore carries little information on extent of gene flow into and among coastal populations.

Are genes faster than crabs? Mitochondrial introgression exceeds larval dispersal during population expansion of the invasive crab Carcinus maenas

Biological invasions offer unique opportunities to investigate evolutionary dynamics at the peripheries of expanding populations. Here, we examine genetic patterns associated with admixture between two distinct invasive lineages of the European green crab, Carcinus maenas L., independently introduced to the northwest Atlantic. Previous investigations based on mitochondrial DNA sequences demonstrated that larval dispersal driven by advective currents could explain observed southward displacement of an admixture zone between the two invasions. Comparison of published mitochondrial results with new nuclear data from nine microsatellite loci, however, reveals striking discordance in their introgression patterns. Specifically, introgression of mitochondrial genomes relative to nuclear background suggests that demographic processes such as sex-biased reproductive dynamics and population size imbalances—and not solely larval dispersal—play an important role in driving the evolution of the genetic cline. In particular, the unpredicted introgression of mitochondrial alleles against the direction of mean larval dispersal in the region is consistent with recent models invoking similar demographic processes to explain movements of genes into invading populations. These observations have important implications for understanding historical shifts in C. maenas range limits, and more generally for inferences of larval dispersal based on genetic data.

A steep genetic cline in yellowtail rockfish, Sebastes flavidus, suggests regional isolation across the Cape Mendocino faunal break

As with all Sebastes species, yellowtail rockfish ( S. flavidus ) produce larvae with an extended pelagic juvenile phase that can be advected in coastal currents. While dispersal potential is high, previous research on population genetic characteristics of Sebastes species indicates that apparent realized dispersal can be much lower and can exhibit complex patterns of genetic structure. We assayed 812 bp of the mitochondrial cytochrome b gene and six microsatellite loci in ∼1000 yellowtail rockfish collected from 21 sites that span the species range from southern California to southeastern Alaska. An abrupt genetic cline near Cape Mendocino, California, splits the range into a northern and southern stock, and is highly concordant between our mitochondrial (FCT = 0.32, p ≪ 0.001) and microsatellite (FCT = 0.02, p ≪ 0.001) datasets. We show that this pattern may be due to a combination of physical (oceanographic or other barriers to larval dispersal), biological (habitat differences), and historical events. This study, and both intra- and inter-specific evidence from other marine species suggests Cape Mendocino demarcates two regions experiencing divergent evolutionary trajectories, and should be considered in management strategies.

Evidence of a genetic cline for Sardina pilchardus along the Northwest African coast

Chlaida, M., Laurent, V., Kifani, S., Benazzou, T., Jaziri, H., and Planes, S. 2009. Evidence of a genetic cline for Sardina pilchardus along the Northwest African coast. – ICES Journal of Marine Science, 66: 264–271. In all, 700 Sardina pilchardus from 14 locations throughout the Atlantic and Mediterranean Moroccan coastlines were screened for eight enzymatic loci that show polymorphism. Analysis of allelic frequencies showed a genetic break in the area of the Bay of Agadir, segregating two groups of samples, confirmed by analysis of molecular variance; a first consisting of Sidi Ifni (29°12′N) and southern samples down to the southern limit of the species in Mauritania (19°03′N 16°28′W), and a second starting in the Bay of Agadir (30°48′N) and consisting of northern samples that appeared homogeneous with the Mediterranean samples. Specifically, a survey of the SOD* loci demonstrated a genetic cline in allelic frequencies along the coastline. Using a clinal variation model under a state of equilibrium, we estimate a dispersal rate of 189 ± 52 km per generation between Mauritania and Ras Kebdana. This major break towards the south of the Bay of Agadir offers a new perspective on the management of sardine, which ideally ought now to be managed as two stocks along the Moroccan coast. The break is most likely induced by hydrodynamic influences that virtually isolate southern from northern populations.

Cellular basis and developmental timing in a size cline of Drosophila melanogaster.

We examined 20 Drosophila melanogaster populations collected from a 2600-km north-south transect in Australia. In laboratory culture at constant temperature and standard larval density, a genetic cline in thorax length and wing area was found, with both traits increasing with latitude. The cline in wing area was based on clines in both cell size and cell number, but was primarily determined by changes in cell number. Body size and larval development time were not associated among populations. We discuss our results in the context of selection processes operating in natural and experimental populations.