Phylogeography of the endangered rosewood Dalbergia nigra (Fabaceae): insights into the evolutionary history and conservation of the Brazilian Atlantic Forest

Abstract

The Brazilian rosewood (Dalbergia nigra) is an endangered tree endemic to the central Brazilian Atlantic Forest, one of the world's most threatened biomes. The population diversity, phylogeographic structure and demographic history of this species were investigated using the variation in the chloroplast DNA (cpDNA) sequences of 185 individuals from 19 populations along the geographical range of the species. Fifteen haplotypes were detected in the analysis of 1297 bp from two non-coding sequences, trnV-trnM and trnL. We identified a strong genetic structure (F ST ¼ 0.62, Po0.0001), with a latitudinal separation into three phylogeographic groups. The two northernmost groups showed evidence of having maintained historically larger populations than the southernmost group. Estimates of divergence times between these groups pointed to vicariance events in the Middle Pleistocene (ca. 350 000-780 000 years ago). The recurrence of past climatic changes in the central part of the Atlantic forest, with cycles of forest expansion and contraction, may have led to repeated vicariance events, resulting in the genetic differentiation of these groups. Based on comparisons among the populations of large reserves and small, disturbed fragments of the same phylogeographic group, we also found evidence of recent anthropogenic effects on genetic diversity. The results were also analysed with the aim of contributing to the conservation of D. nigra. We suggest that the three phylogeographic groups could be considered as three distinct management units. Based on the genetic diversity and uniqueness of the populations, we also indicate priority areas for conservation.

Chloroplast analysis of Zelkova schneideriana (Ulmaceae): genetic diversity, population structure, and conservation implications

“…Therefore, demographic events have played an important role in shaping the genetic diversity of Z. schneideriana. Genetic variety at the cpDNA level mainly existed between populations (F ST = 0.551), which is similar to that previously reported in other endangered plants, such as Dalbergia nigra (Fabaceae, F ST = 0.624) (Ribeiro et al, 2011) and Hymenaea courbaril (Fabaceae, F ST = 0.604) (Ramos et al, 2009). Genetic differences between the populations may have been caused by the limited amount of gene flow (N m = 0.408), due to the species' limited seed dispersal (Fineschi et al, 2002).…”

Diversity and genetic connectivity among populations of a threatened tree (Dalbergia nigra) in a recently fragmented landscape of the Brazilian Atlantic Forest

“…Since this species is a long-lived tree and fragmentation effects are expected to increase over generations (Young et al 1996;Lowe et al 2005), we analyzed and compared adults and saplings. Considering previous studies using allozymes and cpDNA (Ribeiro et al 2005(Ribeiro et al , 2011, we hypothesized that: (1) populations from small and impacted fragments might show lower levels of genetic diversity, (2) genetic depletion might be more pronounced in saplings, and (3) fragmentation might reduce gene flow among populations.…”

“…International trade of its timber has been prohibited since 1992, when D. nigra was listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES 1992). Previous studies of the diversity and genetic structure of this species, using allozyme markers (Ribeiro et al 2005) and chloroplast DNA (cpDNA) sequences (Ribeiro et al 2011), have suggested that this species is sensitive to recent anthropogenic fragmentation.…”

Plastid DNA variation of the endemic species Oxytropis glandulosa Turcz. (Fabaceae)

“…The low level of nucleotide diversity in O. glandulosa (range: 0.0002-0.0059; Table 1) within a total DNA region of 2420 bp is consistent with the low mutation rate in the chloroplast genome that has been estimated for the genus Oxytropis of 8.9 × 10 -10 substitutions per site per year (Wojсiechowski, 2005). Likewise, a low level of nucleotide diversity in cpDNA has been found in endemic legume species such as O. chankaensis (0.0005, Artyukova et al, 2011), Hymenaea stigonocarpa (range: 0-0.0027, Ramos et al, 2007), and Dalbergia nigra (range: 0-0.00084, Ribeiro et al, 2011). The high differentiation of populations in O. glandulosa (Φ ST = 0.758; Table 2) is similar to that in Primula secundiflora Franch.…”

“…ex Benth. (0.752; Ribeiro et al, 2011). Low levels of nucleotide diversity in the Yeravna populations could be due to several factors.…”