Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Abstract

Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.

Keywords: barcoding; biogeography; cryptic species; dispersal; tropical biodiversity.

Figure 1:

Map of Panama indicating major geographic features considered in this study. A) Pink areas are highland regions with greater than 600 meters above sea levels (m.a.s.l) elevation, while light blue show those with less than 300 m.a.s.l. Purple lines indicate the broad geographic areas used to define sampling regions, with names in purple. B) Lowland suture zones. Light yellow shading indicates general locations of suture zones described in this study.

Figure 2:

Phylogenetic sampling of Panamanian birds. Overall avian tree of life modified from Jetz et al (2012). Sampled families are shown in dark blue, with unsampled lineages shown with topology faded out; size of clade scaled by number of species. For each sampled family, dots indicate the number of taxa sampled across multiple regions of Panama (one dot per sampled species). Light purple dots indicate lineages with a single mitochondrial BIN; dark purple indicate those with two or more.

Figure 3:

Geographic distribution of haplotypes in Panamanian birds. Haplotypes were defined initially by BIN for COI data, and then by sequence for additional markers for all taxa with observed mitochondrial breaks, grouped by geographic region of splits. Highland species (A) are separated from lowland birds, and lowland species are displayed by (B) southwest vs rest of Panama, with or without additional splits; (C) splits in both the Veraguas and Darién suture zones; (D) Darién suture zone splits; (E) Veraguas/Colón splits; (F) splits in central Panama, typically around Cerro Azul; (G) lowland taxa which have distinctive haplotypes in east and west, but lack sufficient sampling across the transect to determine the precise locality of the turnover; (H) taxa with idiosyncratic patterns that fit none of the above; and (I) waterbirds, which were generally excluded from analyses due to less consistent sampling. Dot colors indicate distinct BINs, size scaled by the number of samples from a given locality.

Figure 4:

Associations of ecological traits with mitochondrial splits. Throughout the figure, dark purple circles represent taxa with two or more BINs, while light purple indicate those with only one. A) Hand wing index (HWI) is significantly lower in taxa with splits (t= −5.52, df= 154.29, p=<0.001), indicating lower physical dispersal capability is associated with mitochondrial turnover. B) Primary diet, showing that insectivores are represented significantly more than other dietary items (χ²=17.27, df= 7, p=0.02) in taxa with splits. C) A visual representation of habitat use, showing that habitat type as measured by openness (χ²=6.488, df= 2, p=0.039) and stratum (χ²=14.04, df= 4, p=0.007) are associated with mitochondrial turnover, with it becoming increasingly likely in the closed forest understory. D) Despite the relatively even distribution of territoriality across our sample, strongly territorial taxa were overrepresented among those with mitochondrial turnover (χ²=12.04, df= 2, p=0.002).

Figure 5:

Timing of mitochondrial splits for Panamanian birds in millions of years. Time was calculated from pairwise COI divergence (green) and in BEAST2 (purple, shown with median and 95% confidence intervals [CIs]). Splits are grouped by region as in Figure 3, with those taxa with multiple splits being shown for each. Some CIs are truncated due to space (indicated with asterisk); see Table 3 for full details.

Figure 5:

Timing of mitochondrial splits for Panamanian birds in millions of years. Time was calculated from pairwise COI divergence (green) and in BEAST2 (purple, shown with median and 95% confidence intervals [CIs]). Splits are grouped by region as in Figure 3, with those taxa with multiple splits being shown for each. Some CIs are truncated due to space (indicated with asterisk); see Table 3 for full details.