The role of very small fragments in conserving genetic diversity of a common tree in a hyper fragmented Brazilian Atlantic forest landscape

Agricultural Landscape Heterogeneity Matter: Responses of Neutral Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree

Plants are one of the most vulnerable groups to fragmentation and habitat loss, that may affect community richness, abundance, functional traits, and genetic diversity. Here, we address the effects of landscape features on adaptive quantitative traits and evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Caryocar brasiliense. We sampled adults and juveniles in 10 savanna remnants within five landscapes. To obtain neutral genetic variation, we genotyped all individuals from each site using nine microsatellite loci. For adaptive traits we measured seed size and mass and grown seeds in nursery in completely randomized experimental design. We obtained mean, additive genetic variance (V_a) and coefficient of variation (CV_a%), which measures evolvability, for 17 traits in seedlings. We found that landscapes with higher compositional heterogeneity (SHDI) had lower evolutionary potential (CV_a%) in leaf length (LL) and lower aboveground dry mass (ADM) genetic differentiation (Q_ST). We also found that landscapes with higher SHDI had higher genetic diversity (He) and allelic richness (AR) in adults, and lower genetic differentiation (F_ST). In juveniles, SHDI was also positively related to AR. These results are most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Agricultural landscapes with low quality mosaic may be more stressful for plant species, due to the lower habitat cover (%), higher cover of monocropping (%) and other land covers, and edge effects. However, in landscapes with higher SHDI with high quality mosaic, forest nearby savanna habitat and the other environments may facilitate the movement or provide additional habitat and resources for seed disperses and pollinators, increasing gene flow and genetic diversity. Finally, despite the very recent agriculture expansion in Central Brazil, we found no time lag in response to habitat loss, because both adults and juveniles were affected by landscape changes.

Genetic structure and diversity of native Guadua species (Poaceae: Bambusoideae) in natural populations of the Brazilian Amazon rainforest

The Southwestern Region of the Brazilian Amazon is formed by forests dominated by bamboos. The genus Guadua is endemic to the Americas, and little is known about the genetic diversity and structure of species of this genus. This study aimed to evaluate the genetic diversity and structure of two native Guadua species in natural populations in the Southwestern region of the Brazilian Amazon. Therefore, the genetic diversity and structure of Guadua aff. chaparensis and Guadua aff. lynnclarkiae were evaluated with the use of microsatellite molecular markers (SSR). It was verified that the average genetic diversity for the populations studied was considered high ( H ^ e =0.5) compared to other species of bamboo. All populations had rare and private alleles, and none of them presented significant values of inbreeding. The populations were divergent ( G ^ ST = 0.46), resulting in a low apparent gene flow. The Bayesian analysis showed that among the 350 individuals analyzed, five groups (K=5) were formed, with little similarity among the groups (Populations), although two of them presented clonal individuals. According to the results obtained, it can be conclude that populations should be treated as having unique characteristics, mainly when accessed for management and for in situ and ex situ conservation studies.

Potential impact of mammal defaunation on the early regeneration of a large-seeded palm in the Brazilian Atlantic Forest

Defaunation, the decline in animal species and populations, is biased towards large-bodied animals that have unique roles as dispersers of large seeds. However, it is speculated that these roles may still be performed by smaller animals, such as small mammals like rodents and marsupials, that thrive in defaunated sites. We investigated if small mammals can disperse the large-seeded palm Attalea dubia. We performed the study in a well-conserved Atlantic Forest remnant in southeast Brazil that still harbours large mammals, such as tapirs. Focal observations showed that capuchin-monkeys consumed the mesocarp of the fruits and dropped the seeds beneath the plant crown thereafter. Mammals preyed on ca. 1% and removed ca. 15% of the fallen fruit/seed and deposited them up to 15 m away. Amongst them, small mammals (< 1 kg), such as the squirrel Guerlinguetus brasiliensis and non-identified nocturnal Sigmodontinae, as well as the marsupial Philander frenatus performed the bulk of interactions. Dispersal enhances recruitment, but the short distances of seed removal did not match the current spatial distribution of palm seedlings and juveniles. Recaching rates of hoarded seeds were small (2%) and unlikely to increase distances of seed dispersal achieved. Short distances of dispersal would increase plant clumpiness and negative density-dependent effects with time. Although small mammals can provide legitimate dispersal, they cannot fully replace larger frugivorous mammals and maintain long-distance seed dispersal that feeds plant metapopulation dynamics and seed gene flow.

Recent Fragmentation May Not Alter Genetic Patterns in Endangered Long-Lived Species: Evidence From Taxus cuspidata

Forestland fragmentation caused by overexploitation of forest resources can in principle reduce genetic diversity, limit gene flow and eventually lead to species developing strong genetic structure. However, the genetic consequences of recent anthropogenic fragmentation of tree species remain unclear. Taxus cuspidata, which has extremely small populations distributed mainly in Changbai Mt. in Northeast (NE) China, has recently endured severe habitat fragmentation. Here, we investigate the pattern of genetic diversity and structure, identify risk factors, predict the future distribution and finally provide guidelines for the conservation and management of this species. We used three chloroplast and two mitochondrial DNA fragments, which are both paternally inherited in yews but differ in mutation rates, to genotype a total of 265 individuals from 26 populations covering the distribution of the species in China. Both chloroplast and mitochondrial data showed high degrees of genetic diversity, extensive gene flow over the entire geographical range and historical stability of both effective population size and distribution of the species. However, ecological niche modeling suggests a decrease in suitable areas for this species by the years 2050 and 2070. The maintenance of high genetic diversity and the existence of sufficient gene flow suggest that recent fragmentation has not affected the genetic composition of the long-lived tree T. cuspidata. However, severe impacts of anthropogenic activities are already threatening the species. Conservation and management strategies should be implemented in order to protect the remnant populations.

Genetic diversity maintained among fragmented populations of a tree undergoing range contraction

Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analyzed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage-disequilibrium found in the genetic surveys. The two types of estimate were highly correlated. Overall, we found genetic diversity to be only slightly lower in Britain than across a comparable area in Scandinavia where populations are large and continuous. While the ensemble of British fragments maintain diversity levels close to Scandinavian populations, individually they have drifted apart and lost diversity; particularly the smaller populations. An ABC analysis, based on coalescent models, favors demographic scenarios in which Britain maintained high levels of genetic diversity through post-glacial re-colonization. This diversity has subsequently been partitioned into population fragments that have recently lost diversity at a rate corresponding to the current population-size estimates. We conclude that the British population fragments retain sufficient genetic resources to be the basis of conservation and re-planting programmes. Use of markers with different mutation rates gives us greater confidence and insight than one marker set could have alone, and we suggest that RAD-SSRs are particularly useful as high mutation-rate marker set with a well-specified ascertainment bias, which are widely available yet often neglected in existing RAD datasets.

Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw

The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil. We sampled leaves from approximately 24 adult individuals in each of the study sites: two restoration plantations (27 and 62 years old) and two forest remnants. We prepared and sequenced a genotyping-by-sequencing library, SNP markers were identified de novo using Stacks pipeline, and genetic parameters and structure analyses were then estimated for populations. The sequencing step was successful for 80 sampled individuals. Neutral genetic diversity was similar among restored and natural populations (A_R = 1.72 ± 0.005; H_O = 0.135 ± 0.005; H_E = 0.167 ± 0.005; F_IS = 0.16 ± 0.022), which were not genetically structured by population subdivision. In spite of this absence of genetic structure by population we found genetic structure within populations but even so there is not spatial genetic structure in any population studied. Less than 1% of the neutral alleles were exclusive to a population. In general, contrary to our expectations, restoration plantations were then effective for conserving tree genetic diversity in human-modified tropical landscapes. Furthermore, we demonstrate that genotyping-by-sequencing can be a useful tool in restoration genetics.