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Table 1. Population genetic summary metrics used in model validation. n, Sample size; S$, number of segregating sites. The diversity parameter 6 and mean D, across localities are given per base pair (bp). Hs test (23) is used to detect population expansion. BA, Bahia; SP, Sao Paulo refugia. Because predicted refugia were often larger than predicted unstable (recently colonized) areas, n, S,

Table 1 Population genetic summary metrics used in model validation. n, Sample size; S$, number of segregating sites. The diversity parameter 6 and mean D, across localities are given per base pair (bp). Hs test (23) is used to detect population expansion. BA, Bahia; SP, Sao Paulo refugia. Because predicted refugia were often larger than predicted unstable (recently colonized) areas, n, S,

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Fig. 1. Proposed method of biodiversity prediction. Three stages are involved: biodiversity dis- tribution modeling (top), model-based hypothesis formulation (middle), hypothesis testing and model validation (bottom). Distribution models developed under current climatic conditions accurately predict distribu- tions of each of the target species along the Atlantic rainforest domain [area-under-the-curve (AUC) values (16) 0.968, 0.989, and 0.994; maximum Kappa (/7) 0.81, 0.925, and 0.94 in H. albomarginatus, H. faber, and H. semilineatus, respectively (fig. S2)]. Stability maps, depicting the intersection of distribution models for each taxon under current, 6 kybp, and 21 kybp cli- mates, predict for all species a large central re- fugium throughout the Late Quaternary (“Bahia refugium”) (Fig. 2). A second, much smaller refugium is predicted in the northeasternmost portion of the forest (“Pernambuco refugium”). In H. faber, a third, southeastern refugium of intermediate size is also predicted (“Sao Paulo refugium”). This is not surprising, given that this species occupies a broader environmental niche. In contrast to the central and northern regions, populations south of the Bahia or Sao Paulo refugia appear much less stable, despite the more extensive (preclearing) range of the forest in southern and southeastern Brazil. We hypothe- size that these areas received a significant influx of migrants from adjacent, large refugial pop- ulations after the LGM. These palaeomodel re- sults are congruent with the fossil pollen record, which documents a replacement of forests by grasslands in the southern Atlantic forest during the LGM (/4, /8) and suggests the occurrence of small forest refugia in the southernmost range of Metrics of genetic diversity confirm the above patterns (Table 1). In H. albomarginatus and H. semilineatus, genetic diversity (2/) is an order of magnitude larger in the central (Bahia) refugium relative to the less stable (southern) portion of the forest. Diversity of H. faber in this southern area is higher than the other species because of the
Fig. 1. Proposed method of biodiversity prediction. Three stages are involved: biodiversity dis- tribution modeling (top), model-based hypothesis formulation (middle), hypothesis testing and model validation (bottom). Distribution models developed under current climatic conditions accurately predict distribu- tions of each of the target species along the Atlantic rainforest domain [area-under-the-curve (AUC) values (16) 0.968, 0.989, and 0.994; maximum Kappa (/7) 0.81, 0.925, and 0.94 in H. albomarginatus, H. faber, and H. semilineatus, respectively (fig. S2)]. Stability maps, depicting the intersection of distribution models for each taxon under current, 6 kybp, and 21 kybp cli- mates, predict for all species a large central re- fugium throughout the Late Quaternary (“Bahia refugium”) (Fig. 2). A second, much smaller refugium is predicted in the northeasternmost portion of the forest (“Pernambuco refugium”). In H. faber, a third, southeastern refugium of intermediate size is also predicted (“Sao Paulo refugium”). This is not surprising, given that this species occupies a broader environmental niche. In contrast to the central and northern regions, populations south of the Bahia or Sao Paulo refugia appear much less stable, despite the more extensive (preclearing) range of the forest in southern and southeastern Brazil. We hypothe- size that these areas received a significant influx of migrants from adjacent, large refugial pop- ulations after the LGM. These palaeomodel re- sults are congruent with the fossil pollen record, which documents a replacement of forests by grasslands in the southern Atlantic forest during the LGM (/4, /8) and suggests the occurrence of small forest refugia in the southernmost range of Metrics of genetic diversity confirm the above patterns (Table 1). In H. albomarginatus and H. semilineatus, genetic diversity (2/) is an order of magnitude larger in the central (Bahia) refugium relative to the less stable (southern) portion of the forest. Diversity of H. faber in this southern area is higher than the other species because of the
6.2% divergence). In contrast, sites located outside (south of) the refugia are genetically more similar to each other, although to a lesser extent in H. faber (0.1 to 1.6%). Signatures of population expansion (23) are found in the unstable area for H. albomarginatus and H. faber, as well as in the Bahia refugium area for H. faber and H. semilineatus. The lack of signature of 0, and average D, values of the former were obtained not only from the total number of samples, but also from all possible combinations of spatially contiguous localities distributed within the geographic extension of the unstable area. Parentheses encompass minimum and maximum values from subsamples. P values in bold highlight statistical significance at 0.05 probability level.
6.2% divergence). In contrast, sites located outside (south of) the refugia are genetically more similar to each other, although to a lesser extent in H. faber (0.1 to 1.6%). Signatures of population expansion (23) are found in the unstable area for H. albomarginatus and H. faber, as well as in the Bahia refugium area for H. faber and H. semilineatus. The lack of signature of 0, and average D, values of the former were obtained not only from the total number of samples, but also from all possible combinations of spatially contiguous localities distributed within the geographic extension of the unstable area. Parentheses encompass minimum and maximum values from subsamples. P values in bold highlight statistical significance at 0.05 probability level.
Collectively, the results identify the central region as a hotspot within the Atlantic rain- forest hotspot and a refuge for biodiversity during climatic extremes of the Late Pleistocene. This is not to say that southern areas entirely lacked forested habitats in the late Pleistocene: The existence of species and genera endemic to the southern forests (27), as well as some palaeo- ecological and genetic evidence (28), offer evidence to the contrary. Rather, the phylogeographically validated palaeomodels presented here show that the central region had much higher stability relative to the south. Forest lizards (/4, 29) and birds (30) also show high diversity in the central portion of the biome relative to southern areas, and provide evidence for population expansion in southern regions. This reassures us that the pro- cesses uncovered by the amphibian data may be generalized to and help to explain patterns of be efugium (population 2). (8) and (D) Postisolation migration not included in model; (C) and (E) postisolation migration included in model. To test for assemblage-wide colonization of predicted unstable areas, we group mtDNA sequences from the southernmost refugial sites [population 1 (Fig. 3A)] and from localities in unstable areas south of the refugium [population 2 (Fig. 3A)] to contrast two alternative historical models across the three codistributed species, while allowing the taxon-specific demographic parameters to vary. In Hy, the long-term persist- ence model, two contemporary populations split from an ancestral population prior to the LGM (120,000 to 1.2 million years before present, or Mybp, Fig. 3A). In H:, the recent colonization model, population 2 is modeled as being colo- nized from refugial population 1 subsequent to Relative to nuclear loci, mtDNA data are more variable and readily collected and often provide key insights into biological response to environmental modification (/). Although single- locus inference can be imprecise in the face of coalescent variance and the possibility of selec- tion (26), our method benefits from a multitaxon approach, while explicitly accounting for the
Collectively, the results identify the central region as a hotspot within the Atlantic rain- forest hotspot and a refuge for biodiversity during climatic extremes of the Late Pleistocene. This is not to say that southern areas entirely lacked forested habitats in the late Pleistocene: The existence of species and genera endemic to the southern forests (27), as well as some palaeo- ecological and genetic evidence (28), offer evidence to the contrary. Rather, the phylogeographically validated palaeomodels presented here show that the central region had much higher stability relative to the south. Forest lizards (/4, 29) and birds (30) also show high diversity in the central portion of the biome relative to southern areas, and provide evidence for population expansion in southern regions. This reassures us that the pro- cesses uncovered by the amphibian data may be generalized to and help to explain patterns of be efugium (population 2). (8) and (D) Postisolation migration not included in model; (C) and (E) postisolation migration included in model. To test for assemblage-wide colonization of predicted unstable areas, we group mtDNA sequences from the southernmost refugial sites [population 1 (Fig. 3A)] and from localities in unstable areas south of the refugium [population 2 (Fig. 3A)] to contrast two alternative historical models across the three codistributed species, while allowing the taxon-specific demographic parameters to vary. In Hy, the long-term persist- ence model, two contemporary populations split from an ancestral population prior to the LGM (120,000 to 1.2 million years before present, or Mybp, Fig. 3A). In H:, the recent colonization model, population 2 is modeled as being colo- nized from refugial population 1 subsequent to Relative to nuclear loci, mtDNA data are more variable and readily collected and often provide key insights into biological response to environmental modification (/). Although single- locus inference can be imprecise in the face of coalescent variance and the possibility of selec- tion (26), our method benefits from a multitaxon approach, while explicitly accounting for the
Related topics:
GeographyDemographyClimate ChangeBiodiversityEcological Niche ModelingAtlantic ForestConservation of Natural ResourcesMolecular Sequence Data
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