Local climate and vernalization requirements explain the latitudinal patterns of flowering initiation in the crop wild relative Linum bienne

Background and Aims: Days to flowering initiation in species with large geographic distributions often correlate with latitude. Latitude reflects climatic gradients, but it is unclear if large-scale differentiation in flowering results from adaptation to local climate, and whether adaptation to local climate could constrain shifts in distribution and colonization of new environments. Methods: In its Western range in Europe, L. bienne populations were surveyed to describe latitudinal patterns of flowering initiation and determine its correlation with the local climate of populations. This was measured under standardized greenhouse conditions, with a vernalization experiment to learn if chilling advances flowering, and with a reciprocal transplant experiment at three sites along the latitudinal gradient, recording flowering at the central site and plant survival in all sites. Also, genetic differentiation of populations along the latitudinal range was studied using microsatellite markers. Key Results: Flowering initiation varied with latitude, with southern populations flowering earlier than northern populations. Latitude also predicted population response to vernalization, with chilling inducing a greater advance of flowering initiation in northern than southern populations. In general, plant survival in the reciprocal transplant experiment decreased with the geographic distance of populations to the experimental site and, at the central site, flowering initiation varied with latitude of origin. However, across experiments, the local climate of populations better predicted the differentiation in flowering initiation and vernalization response than latitude of origin. Finally, the microsatellite data revealed genetic differentiation of populations forming two groups that agree with a Mediterranean and Atlantic lineage. Conclusions: The consistent result across experiments of a latitudinal cline in flowering initiation and in the vernalization response suggests that flowering is under genetic regulation and yet dependent on particular environmental and climatic cues at local scale. However, the genetic differentiation suggests that past population history might influenced the flowering initiation patterns detected.

Low Genetic Connectivity of Strongly Inbred Ruppia brevipedunculata in Aquaculture Dominated Lagoons (Viet Nam)

Lagoonal environments exhibit high levels of instability depending on hydrological, climatic and ecological factors, thereby influencing the distribution and structure of submerged plant communities. Conditions typically fluctuate widely due to the interaction of freshwater from rivers with saltwater from the sea, as well as from aquaculture activities that together influence submerged hydrophyte community spatial and temporal variability depending on plant survival strategies. Ruppia species feature either underwater pollination mediated by an air bubble or by the release of pollen floating at the water surface, the former promoting self-pollination. Tropical Asian Ruppia brevipedunculata Yu and den Hartog was assumed to pollinate below the water surface and identified as a separate lineage among selfed Ruppia taxa. We used nine nuclear microsatellites to estimate inbreeding levels and connectivity of R. brevipedunculata within a large SE Asian lagoon complex. Ruppia brevipedunculata meadows were strongly inbred as could be derived from the many monomorphic or totally fixed loci for unique alleles in different parts of the lagoon, which appears consistent with selfing behavior. Those from aquaculture ponds were highly inbred (FIS = 0.620), though less than open lagoon sites that showed nearly total inbreeding (FIS = 0.942). Ruppia brevipedunculata from two major lagoon parts were highly differentiated with spatially structured gene pools and a strong barrier between parts of the lagoon over a 30 km distance. Migration-n analysis indicated unidirectional though limited gene flow and following potential hydrological connectivity. Overall, private alleles under homozygote conditions explained a stronger genetic differentiation of populations situated inside aquaculture ponds than of open lagoon populations. Kinship values were only relevant up to 5 km distance in the open lagoon. Within a confined area of aquaculture ponds featuring dense vegetation in stagnant water, there would be opportunity for mixed pollination, thereby explaining the higher diversity of unique multilocus genotypes of aquaculture pond habitats. Low connectivity prevents gene pools to homogenize however promoted sites with private alleles across the lagoon. Complex hydrodynamic systems and human-made habitats enclosed by physical structures impose barriers for propagule dispersal though may create refugia and contribute to conserving regional genetic diversity.

Assessment of genetic differentiation of populations by analysis of molecular variance (analytical review)

Different approaches to using the analysis of molecular variance (AMOVA) to assess the genetic differentiation of populations have been compared in the research. Data on 11 microsatellite loci of 84 bulls of seven breeds were used. The results were compared for three options of the AMOVA module of the GenAlEx 6.502 program: the allele distance matrix (calculated FST(W&C)(=θ) statistics – variant AMOVA1); the genotype distance matrix (ΦPT– AMOVA2); and the allele size difference matrix (RST– AMOVA3). Similar summary estimates of the genetic differentiation of breeds were obtained: FST(W&C)= 0.108, ΦPT= 0.115, RST= 0.110 (all with pperm≤ 0.001). Between the estimates of FST(W&C)and ΦPTfor each locus, the correlation coefficient was 0.99 (pvalue<0.0001); no statistically significant correlations with RSTwere found. A high correlation of FST(W&C)and ΦPTwith the estimates of differentiation according to Nei’s (0.96) was found. Programs other than GenAlEx (Arlequin v.3.5, GenePop v.4.7.3, RST22) gave similar AMOVA estimates. The negative linear dependence of FST(W&C)and ΦPTon the level of the average heterozygosity of the breed samples was established (R2= 0.6, rS= -0.75 for pvalue < 0.02) and the absence of such dependence for RST(R2= 0.04, rS= -0.23 for pvalue= 0.47). The standardization of the FST(W&C)and ΦPTestimates according to Hedrick’s eliminated this dependence and raised the initial estimates to 0.35 and 0.37, respectively. The latter were comparable to the estimates obtained by the Nei-Hedrick’s (0.364-0.375), Jost’s (0.292), and Morisit-Horn’s (0.308) methods. The Mantel correlations between the matrices of paired genetic distances (GD) calculated by different measures were >0.9 in most cases. The projections of the GD matrices in the principal coordinate analysis (PCoA) on the 2D plane were generally similar. The PCoA identified a cluster of Holstein «ecotypes», a cluster of «Red» breeds, and a branch of the Jersey breed. In the two-factor AMOVA of data on clusters (as two «regions»), the interregional GD was 0.357; the differentiation of breeds within the «regions» did not exceed 0.027. Modeling the association of breeds with close to zero GD resulted in an increase in the number of alleles per locus in the «new» breeds by 29 %, and an increase in the combined estimate of genetic differentiation by 29-46 %. The results obtained can be used in the development of measures for the conservation of endangered breeds.

GENETIC DIFFERENTIATION BY STR-MARKERS AND PRODUCTIVITY TRAITS OF KARACHAEV GOATS FROM DIFFERENT BREEDING ZONES

Data have been obtained indicating differences by the live weight and exterior appearance of Karachaev goats bred in the mountain area, foothill, and plain-hill zone. A high level of genetic diversity and a clear genetic differentiation of populations from different breeding zones on the basis of STR-markers have been established.

Past and future sky-island dynamics of tropical mountains: A model for two Geotrupes (Coleoptera: Geotrupidae) species in Oaxaca, Mexico

Recent collecting and taxonomic studies of dung beetles of the genus Geotrupes Latreille (Coleoptera: Geotrupidae) in the mountains of Oaxaca have evidenced the existence of a vicariant speciation pattern, where one species occupies the northern mountain system and the other one the southern mountain range. A study of this possible vicariant speciation mechanism is presented using a paleobiogeographic mapping analysis of both Geotrupes species distribution during Late Quaternary glaciation events. Based on these paleomaps a possible speciation mechanism (vicariant speciation) is suggested, in which one common ancestor (mother species) lived at the bottom of the Valle de Oaxaca (Oaxaca Valley) during the last local glacial maximum (LLGM, 21-17.5 kyr) and whose possible continuous distribution was broken into two (or more) separated areas on mountaintops as the climate became warmer toward the present. We propose that the fragmentation and isolation of habitats may have promoted genetic differentiation of populations resulting in vicariant speciation, as suggested by a sky-island dynamic process. The example of a possible effect of the Little Ice Age in the mountains of Oaxaca is also discussed. Finally, a projection is made into the XXII century, based on climatic modeling predictions. These last results suggest the possible disappearance of the sky-island dynamic process through the accelerated speed of climatic change.

Phylogeography of the widespread white-eared hummingbird (Hylocharis leucotis): pre-glacial expansion and genetic differentiation of populations separated by the Isthmus of Tehuantepec

The Pleistocene glacial cycles had a strong influence on the demography and genetic structure of many species, particularly on northern-latitude taxa. Here we studied the phylogeography of the white-eared hummingbird (Hylocharis leucotis), a widely distributed species of the highlands of Mexico and Central America. Analysis of mitochondrial DNA (mtDNA) sequences was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. Analyses of 108 samples from 11 geographic locations revealed population structure and genetic differentiation among populations separated by the Isthmus of Tehuantepec (IT) and the Motagua-Polochic-Jocotán (MPJ) fault barriers. ENM predicted a widespread distribution of suitable habitat for H. leucotis since the Last Inter Glacial (LIG), but this habitat noticeably contracted and fragmented at the IT. Models for historical dispersal corridors based on population genetics data and ENM revealed the existence of corridors among populations west of the IT; however, the connectivity of populations across the IT has changed little since the LIG. The shallow geographic structure on either side of the isthmus and a star-like haplotype network, combined with the long-term persistence of populations across time based on genetic data and potential dispersal routes, support a scenario of divergence with migration and subsequent isolation and differentiation in Chiapas and south of the MPJ fault. Our findings corroborate the profound effects of Pleistocene climatic fluctuations on the evolutionary history of montane taxa but challenge the generality of expanded suitable habitat (pine-oak forests) during glacial cycles.

Genetic differentiation is determined by geographic distance in Clarkia pulchella

Both environmental differences and geographic distances may contribute to the genetic differentiation of populations on the landscape. Understanding the relative importance of these drivers is of particular interest in the context of geographic range limits, as both swamping gene flow and lack of genetic diversity are hypothesized causes of range limits. We investigated the landscape genetic structure of 32 populations of the annual wildflower Clarkia pulchella from across the species’ geographic range in the interior Pacific North-west. We tested whether climatic differences between populations influenced the magnitude of their genetic differentiation. We also investigated patterns of population structure and geographic gradients in genetic diversity. Contrary to our expectations, we found an increase in genetic diversity near the species’ northern range edge. We found no notable contribution of climatic differences to genetic differentiation, indicating that any processes that might operate to differentiate populations based on temperature or precipitation are not affecting the putatively neutral loci in these analyses. Rather, these results support seed and pollen movement at limited distances relative to the species’ range and that this movement and the subsequent incorporation of immigrants into the local gene pool are not influenced by temperature or precipitation similarities among populations. We found that populations in the northern and southern parts of the range tended to belong to distinct genetic groups and that central and eastern populations were admixed between these two groups. This pattern could be the result of a past or current geographic barrier associated with the Columbia Plateau, or it could be the result of spread from separate sets of refugia after the last glacial maximum.