Aim Historical and geological events can impact the genetic structure of species, producing signatures that vary among taxa and among gene pools within taxa. Such signatures can also be affected by local geography and tolerance to environmental conditions. However, disentangling the different drivers of population structure is often difficult. In an attempt to do so, we surveyed two independent gene pools of the same species that followed similar paths of post‐glacial colonization across contrasting landscapes and environmental conditions. We aimed to determine how these differences have affected the post‐glacial population dynamics of each gene pool. Location The Pacific and Atlantic coasts of Mexico. Taxon Black mangrove (Avicennia germinans; Avicenniaceae). Methods Using microsatellite variation, we estimated the divergence time of black mangrove populations through approximated Bayesian computation and implemented a comparative approach to evaluate different demographic hypotheses within and between coasts. Results The Pacific and Atlantic gene pools diverged long after the rise of the Central American Isthmus (Mid‐Pleistocene), although occasional transisthmian gene exchanges were also inferred. Both coasts showed the characteristic isolation by distance (IBD) pattern expected for expanding gene pools. However, populations from the Atlantic coast were more genetically diverse and admixed than those from the Pacific basin. Both our migration models and the climate data gathered suggested a more ancient establishment and/or more stable conditions for black mangrove on the Atlantic coast. Main conclusions The Atlantic basin likely bore more favourable climate conditions than the Pacific, allowing for the survival of A. germinans during the Last Glacial Maximum in situ. Populations from the northern Pacific coast became established after the Holocene warming, leading to contrasting genetic patterns between the two gene pools. Nevertheless, the action of environmental factors in determining the contemporary distribution of genetic variation in A. germinans cannot be discarded.

The niche-centroid hypothesis states that populations that are distributed near the centroid of the species' ecological niche will have higher fitness-related attributes, such as population abundance and genetic diversity than populations near the edges of the niche. Empirical evidence based on abundance and, more recently, genetic diversity data support this hypothesis. However, there are few studies that test this hypothesis in coastal species, such as mangroves. Here, we focused on the black mangrove Avicennia germinans. We combined ecological, heterozygosity, and allelic richness information from 1,419 individuals distributed in 40 populations with three main goals: (1) test the relationship between distance to the niche centroid and genetic diversity, (2) determine the set of environmental variables that best explain heterozygosity and allelic richness, and (3) predict the spatial variation in genetic diversity throughout most of the species' natural geographic range. We found a strong correlation between the distance to the niche centroid and both observed heterozygosity (Ho; ρ2 = 0.67 P < 0.05) and expected heterozygosity (He; ρ2 = 0.65, P < 0.05). The niche variables that best explained geographic variation in genetic diversity were soil type and precipitation seasonality. This suggests that these environmental variables influence mangrove growth and establishment, indirectly impacting standing genetic variation. We also predicted the spatial heterozygosity of A. germinans across its natural geographic range in the Americas using regression model coefficients. They showed significant power in predicting the observed data (R2 = 0.65 for Ho; R2 = 0.60 for He), even when we considered independent data sets (R2= 0.28 for Ho; R2 = 0.25 for He). Using this approach, several genetic diversity estimates can be implemented and may take advantage of population genomics to improve genetic diversity predictions. We conclude that the level of genetic diversity in A. germinans is in agreement with expectations of the niche-centroid hypothesis, namely that the highest heterozygosity and allelic richness (the basic genetic units for adaptation) are higher at locations of high environmental suitability. This shows that this approach is a potentially powerful tool in the conservation and management of this species, including for modelling changes in the face of climate change.

Special conservation efforts should be made for relict species, as they usually have small population sizes and restricted distributions, placing them in critical extinction risk. To achieve conservation, information about genetic diversity distribution is needed. Here, using nine nuclear microsatellites, we analyzed 23 populations of five recently described species of Magnolia distributed in Mexico, which were previously assigned to Magnolia dealbata. We aimed to determine the level of genetic diversity and the distribution of genetic variation and proposed conservation measures. Compared to other endemic and relict species, we found a moderate level of genetic diversity in most populations; however, we identified two populations with no genetic variation. Additionally, we found evidence of positive values of inbreeding likely due to geitonogamy. We found a strong population structure, low effective population size, and no evidence of bottlenecks. Patterns of genetic differentiation did not support the morphological distinction of five species, so we hypothesized that the gene pools may instead represent well-differentiated populations of a single species. We argue that the pattern of genetic differentiation is explained by the natural fragmentation of the cloud forests after glaciation events, and the effects of genetic drift in small populations poorly connected by gene flow. Despite the moderate levels of genetic diversity, special attention is needed to guarantee conservation, with emphasis on the populations in the central region of the country as well as the valuable populations identified in the southwestern region.