Estimating population structure under nonequilibrium conditions in a conservation context: continent‐wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae)

Abstract

Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.

Disruption of historical patterns of isolation by distance in coastal steelhead

“…salmonids (Palstra et al 2007), including California steelhead (Garza et al 2004;Pearse et al 2007), cod (Pogson et al 2001), oysters (Peterson and Denno 1998), insects (Rose et al 2006), and plants (CruseSanders and Hamrick 2004), but see Pearse et al (2006) for an exception in turtles). However, without a historical reference point, there is no way to know if the populations are in migration-drift equilibrium or representative of their natural state.…”

Extremely low genetic diversity and weak population differentiation in the endangered Colombian river turtle Podocnemis lewyana (Testudines: Podocnemididae)

“…Vargas-Ramírez et al (2007) studied a 488-bp-long fragment of the mitochondrial cytochrome b gene in 109 individuals from five regions in the Magdalena and Sinú River Basins and found only two haplotypes, differing by only one substitution. By contrast, in two other Podocnemis species high levels of genetic diversity were discovered with mtDNA and microsatellite data (Pearse et al 2006;Escalona et al 2009). In the present study, we use rapidly evolving nuclear and mitochondrial markers [microsatellites, variable part of the control region (CR)] and a range-wide sampling to assess population genetic structure, bottlenecks, gene flow, and population expansion in P. lewyana.…”

Short Communication Population genetics analysis of Podocnemis sextuberculata (Testudines, Podocnemidae): lack of population structure in the central Amazon Basin

“…The low levels of genetic variability found for the partial sequence of the ND1 gene in P. sextuberculata (Table 2) are consistent with those suggested by Avise et al (1992) for the low rate of molecular evolution of mtDNA in turtles compared with other taxa. However, such a suggestion may be more frequent for coding genes, since non-coding regions, as observed in ribosomal genes and mitochondrial control region, have been broadly used for analyses of population level (Seddon et al, 1998;Sites Jr. et al, 1999;Pearse et al, 2006a). Protein-coding genes, such as cytochrome b, have been characterized as relatively invariable in E. marmorata (Janzen et al, 1997) and P. lewyana (Vargas-Ramírez et al, 2007), although they have shown sufficiently high variation for phylogeographic analyses in other species, such as in North American softshell turtles Apalone spp (Weisrock and Janzen, 2000).…”

“…More recently, P. lewyana, a species endemic to northern Colombia, has been genetically characterized using the cytochrome b gene (Vargas-Ramírez et al, 2007), and the mating system of P. unifilis has been studied with microsatellite DNA markers (Fantin et al, 2008). In the study of P. expansa from the Amazon Basin, Pearse et al (2006a) utilized mitochondrial and microsatellite markers in individuals drawn from various hydrographic basins. The authors found a lack of population structure in tributaries of the same hydrographic basin, but genetic differences among basins.…”