**6. Conclusions**

In conclusion, the separation of the northern and southern phylogroups observed at Atlantic Forest endemic species is a pattern found for several taxa, however the discontinuities were observed in distinct zones of the Atlantic Forest. Some discrepancies can be explained by sampling bias, but others can be due to real differences in the dynamics of the species or the associated ecosystem. Anyway, distinct mechanisms have been invoked to explain the breaks, sometimes they were attributed differences are attributed to refuges hypothesis and another times to riverine barriers or tectonic activities. Silva et al. (in press) studied the panbiogeographic nodes in Atlantic Forest found six of the seven nodes found one node (Pernambuco) in North AF, two nodes (Bahia and Espírito Santo) are in Central AF, and three nodes (São Paulo, Paraná and Santa Catarina) correspond to South AF and concluded that the pattern of latitudinal subdivision of *taxa* distributions has originated at least since the Miocene and is more complex than previously thought. The endemism areas are concordant with the stability areas proposal for Atlantic Forest, the great part of studies show differentiation between lineages in Pleistocene Epoch (Table 1). Due to the complexity of the geomorphological and ecological features of the Atlantic Forest, and the intrinsic complexity of the ecophysiology of the Atlantic Forest organisms, it seems too simplistic to imagine that one single diversification mechanism can explain the origin of the current biogeographical patterns exhibit by Atlantic Forest species (D´Horta et al. 2011). A realist scrutiny of the Atlantic Forest diversity and past ecosystem dynamics should consider multiple mechanisms operating at different spatial and temporal scales (Thomé et al. 2010).

The elucidating the process that acted in Atlantic forest is essential to understand the biodiversity present in this biome, and to conservation of lineages and species. Understanding the speciation process, the effects of climate oscilations will be important to estimate the consequence of global warming in this ecosystem. Predictions of ecological niche modeling to Brazil has indicated a decline of 80% of current distribution for half of the birds of the family Pipridae in Amazon and Atlantic Florest (Anciães & Peterson, 2006). Niches paleoclimate modeling combined with molecular analysis has pointed to cases of recent population expansion from refuges or ecologically stable areas with high diversity and population structure in the Atlantic in response to environmental changes in the Quaternary Period: amphibians, lizards (Carnaval et al. 2009, Carnaval and Moritz 2008) and birds (Cabanne *et al.*, 2008). Thus, the importance of the characterization of the distribution of the genetic diversity of threatened and non-threatened species is important to future conservation plans and politics efforts.
