Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland

Nishikawa, Kanto; Matsui, Masafumi; Yong, Hoi Sen; Ahmad, Norhayati; Yambun, Paul; Belabut, Daicus M.; Sudin, Ahmad; Hamidy, Amir; Orlov, Nikolai L.; Ota, Hidetoshi; Yoshikawa, Natsuhiko; Tominaga, Akira; Shimada, Takehiko

doi:10.1016/j.ympev.2012.02.017

Cited by 32 publications

(47 citation statements)

References 52 publications

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“…However, the only published study of intraspecific caecilian genetics ( Ichthyophis sp. from the Western Ghats of India) suggests that caecilians are not necessarily philopatric [95], although a more recent study from Southeast Asia suggests much higher structuring over a far smaller area [96]. The strong population genetic structure shown in our study, together with the large number of private alleles, is therefore more in line with this and the traditional view of amphibians, and is somewhat extreme given the small size of the island and almost ubiquitous occupancy of this species on São Tomé (RCD, GJM & RES pers.…”

Section: Discussionmentioning

confidence: 98%

Population Genetics of the São Tomé Caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) Reveals Strong Geographic Structuring

2014

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Islands provide exciting opportunities for exploring ecological and evolutionary mechanisms. The oceanic island of São Tomé in the Gulf of Guinea exhibits high diversity of fauna including the endemic caecilian amphibian, Schistometopum thomense. Variation in pigmentation, morphology and size of this taxon over its c. 45 km island range is extreme, motivating a number of taxonomic, ecological, and evolutionary hypotheses to explain the observed diversity. We conducted a population genetic study of S. thomense using partial sequences of two mitochondrial DNA genes (ND4 and 16S), together with morphological examination, to address competing hypotheses of taxonomic or clinal variation. Using Bayesian phylogenetic analysis and Spatial Analysis of Molecular Variance, we found evidence of four geographic clades, whose range and approximated age (c. 253 Kya – 27 Kya) are consistent with the spread and age of recent volcanic flows. These clades explained 90% of variation in ND4 (φCT = 0.892), and diverged by 4.3% minimum pairwise distance at the deepest node. Most notably, using Mismatch Distributions and Mantel Tests, we identified a zone of population admixture that dissected the island. In the northern clade, we found evidence of recent population expansion (Fu's Fs = −13.08 and Tajima's D = −1.80) and limited dispersal (Mantel correlation coefficient = 0.36, p = 0.01). Color assignment to clades was not absolute. Paired with multinomial regression of chromatic data, our analyses suggested that the genetic groups and a latitudinal gradient together describe variation in color of S. thomense. We propose that volcanism and limited dispersal ability are the likely proximal causes of the observed genetic structure. This is the first population genetic study of any caecilian and demonstrates that these animals have deep genetic divisions over very small areas in accordance with previous speculations of low dispersal abilities.

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Section: Discussionmentioning

confidence: 98%

Population Genetics of the São Tomé Caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) Reveals Strong Geographic Structuring

2014

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“…Two reflect the basal split within the Ichthyophiidae (Gower et al 2002) and correspond roughly to groups that have often been treated separately in higher classification because they are morphologically very distinct (e.g. Nussbaum and Wilkinson 1989;Wilkinson and Nussbaum 2006) and which we refer to informally here as the ichthyophiines, comprising all but one species of Ichthyophis (including species of the recently synonymised Caudacaecilia (Nishikawa et al 2012)) and the uraeotyphlines (comprising Ichthyophis bombayensis and all Uraeotyphlus spp.). Because only one species of the newly discovered family Chikilidae (Kamei et al 2012) was available for inclusion in this study, it is included in these analyses with its sister group Herpelidae (Kamei et al 2012).…”

Section: Study Samples and Phylogenymentioning

confidence: 93%

Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

et al. 2014

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Insights into morphological diversification can be obtained from the ways the species of a clade occupy morphospace. Projecting a phylogeny into morphospace provides estimates of evolutionary trajectories as lineages diversified information that can be used to infer the dynamics of evolutionary processes that produced patterns of morphospace occupation. We present here a large-scale investigation into evolution of morphological variation in the skull of caecilian amphibians, a major clade of vertebrates. Because caecilians are limbless, predominantly fossorial animals, diversification of their skull has occurred within a framework imposed by the functional demands of head-first burrowing. We examined cranial shape in 141 species, over half of known species, using X-ray computed tomography and geometric morphometrics. Mapping an existing phylogeny into the cranial morphospace to estimate the history of morphological change (phylomorphospace), we find a striking pattern: most species occupy distinct clusters in cranial morphospace that closely correspond to the main caecilian clades, and each cluster is separated by unoccupied morphospace. The empty spaces in shape space are unlikely to be caused entirely by extinction or incomplete sampling. The main caecilian clades have different amounts of morphological disparity, but neither clade age nor number of species account for this variation. Cranial shape variation is clearly linked to phyletic divergence, but there is also homoplasy, which is attributed to extrinsic factors associated with head-first digging: features of caecilian crania that have been previously argued to correlate with differential microhabitat use and burrowing ability, such as subterminal and terminal mouths, degree of temporal fenestration (stegokrotaphy/ zygokrotaphy), and eyes covered by bone, have evolved and many combinations occur in modern species. We find evidence of morphological convergence in cranial shape, among species that have eyes covered by bone, resulting in a narrow bullet-shaped head. These results reveal a complex history, including early expansion of morphospace and both divergent and convergent evolution resulting in the diversity we observe today.

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“…Caecilians (Gymnophiona), an evolutionarily and morphologically distinct lineage of amphibians, are particularly understudied (but see Zardoya & Meyer 2001;San Mauro et al 2004;Zhang & Wake 2009;Nishikawa et al 2012;Stoelting et al 2014); given their cryptic subterranean lifestyle, there is much to be learned from molecular ecological studies of these elusive tropical amphibians. Likewise, comparatively little molecular ecology work has been conducted on direct-developing amphibians.…”

Section: Future Directions and Critical Knowledge Gapsmentioning

confidence: 99%

Amphibian molecular ecology and how it has informed conservation

McCartney‐Melstad

Shaffer

2015

Molecular Ecology

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Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.

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Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland

Cited by 32 publications

References 52 publications

Population Genetics of the São Tomé Caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) Reveals Strong Geographic Structuring

Population Genetics of the São Tomé Caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) Reveals Strong Geographic Structuring

Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

Amphibian molecular ecology and how it has informed conservation

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