Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

Abstract

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

Fig 1. Main vegetation zones and rivers in the Ecuadorian northwest.

The map is a simplified version of the main vegetation zones of Sierra [55].

Fig 2. Bayesian consensus phylogram depicting relationships within bothropoid pitvipers.

The phylogram was derived from analysis of 2908 bp of mitochondrial DNA (gene fragments 12S, 16S, Cytb and ND4). Posterior probabilities and voucher numbers are shown.

Fig 3. Bayesian consensus phylogram depicting relationships within the genus Alopoglossus.

The phylogram was derived from analysis of 1139 bp of mitochondrial DNA (gene fragments 12S, 16S, Cytb and ND4). Posterior probabilities and voucher numbers are shown.

Fig 4. Bayesian consensus phylogram depicting relationships within the Pristimantis (Hypodictyon) rubicundus species series.

The phylogram was derived from analysis of 1032 bp of mitochondrial DNA (gene fragments 12S and 16S). Posterior probabilities and voucher numbers are shown.

Fig 5. Bayesian consensus phylogram depicting relationships within the Pristimantis lacrimosus species group.

The phylogram was derived from analysis of 2598 bp of mitochondrial DNA (gene fragments 12S and 16S). Posterior probabilities and voucher numbers are shown.

Fig 6. Bayesian consensus phylogram depicting relationships of the yellow-groined Trans-Andean Pristimantis of Ecuador.

The phylogram was derived from analysis of 1905 bp of mitochondrial DNA (gene fragments 12S and 16S). Posterior probabilities and voucher numbers are shown.

Fig 7. Distribution of the sister species Bothrops osbornei and B. punctatus in Ecuador.

White dots represent known localities. Each colored area is a geographic representation of the suitable environmental conditions for one of the clades recovered in the phylogeny of Fig 2.

Fig 8. Distribution of the sister species Alopoglossus festae and A. viridiceps in Ecuador.

White dots represent known localities. Each colored area is a geographic representation of the suitable environmental conditions for one of the clades recovered in the phylogeny of Fig 3.

Fig 9. Distribution of the sister species Pristimantis labiosus and P. crenunguis in Ecuador.

White dots represent known localities. Each colored area is a geographic representation of the suitable environmental conditions for one of the clades recovered in the phylogeny of Fig 4.

Fig 10. Distribution of the sister species Pristimantis mindo and B. subsigillatus in Ecuador.

White dots represent known localities. Each colored area is a geographic representation of the suitable environmental conditions for one of the clades recovered in the phylogeny of Fig 5.

Fig 11. Distribution of Pristimantis buenaventura, P. luteolateralis, P. nietoi and P. walkeri in Ecuador.

White dots represent known localities. Each colored area is a geographic representation of the suitable environmental conditions for one of the clades recovered in the phylogeny of Fig 6.

Fig 12. Morphological variation within sampled Bothrops species.

(a) Juvenile of B. punctatus (ANF 1575). (b) Adult (ANF 2101) of B. punctatus. (c) Juvenile of B. osbornei (ANF 2005). (d) Adult of B. osbornei (ANF 2767).

Fig 13. Morphological variation within sampled Alopoglossus species.

(a) Adult male of A. viridiceps (MZUTI 3552). (b) Juvenile of A. festae (MZUTI 2630). (c) Adult of A. festae (MZUTI 2994). (d) Adult female of A. festae (MZUTI 3370).

Fig 14. Morphological variation within Pristimantis crenunguis and P. labiosus.

(a) Juvenile of Pristimantis crenunguis (Not vouchered). (b) Adult of P. crenunguis (Not vouchered). (c) Juvenile of P. labiosus (MZUTI 3511). (d) Adult of P. labiosus (Not vouchered).

Fig 15. Morphological variation within Pristimantis subsigillatus and P. mindo.

(a) Adult male of Pristimantis subsigillatus (MZUTI 2228). (b) Adult female of P. subsigillatus (MZUTI 2653). (c) Adult male of P. mindo (MZUTI 1382). (d) Adult female of P. mindo (MZUTI 1766).

Fig 16. Pristimantis walkeri species complex and similar species.

(a) Adult male paratype of Pristimantis buenaventura (MZUTI 3270). (b) Adult male holotype of P. buenaventura (MZUTI 3480). (c) Adult female paratype of P. buenaventura (MZUTI 3356). (d) Adult male holotype of P. nietoi (MZUTI 3913). (e) Adult male paratype of P. nietoi (MZUTI 3914). (f) Adult male paratype of P nietoi (MZUTI 3915). (g) Adult male of P. luteolateralis (MZUTI 3092. (h) Adult male of P. luteolateralis (MZUTI 3904). (i) Adult female of P. luteolateralis (Not vouchered). (j) Adult male of P. parvillus (Not vouchered). (k) Adult male of P. walkeri (MZUTI 1768). (l) Adult female of P. walkeri (Not vouchered). (m) Adult female of P. scolodiscus (Not vouchered). (n) Adult male of P. esmeraldas (MZUTI 3545). (o) Adult female of P. esmeraldas (MZUTI 3375).

Fig 17. Adult male holotype of Pristimantis nietoi.

MZUTI 3913, SVL 16.3 mm.

Fig 18. Pristimantis nietoi in life.

MZUTI 3913, SVL 16.3 mm, adult male, holotype.

Fig 19. Adult male holotype of Pristimantis buenaventura.

MZUTI 3480, SVL 19.2 mm.

Fig 20. Pristimantis buenaventura in life.

MZUTI 3480, SVL 19.2 mm, adult male, holotype.

Fig 21. Color variation in the type series of Pristimantis buenaventura.

From left to right, these are: MZUTI 3356, MECN 11337, 11338, MZUTI 3480, MECN 11333, 11339, 11335. Females are shown in the first row.