Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes.

Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.

Imperfect morphological convergence: variable changes in cranial structures underlie transitions to durophagy in moray eels.

Convergence is central to the study of evolution because it demonstrates the power of natural selection to deterministically shape phenotypic diversity. However, the conditions under which a common morphology repeatedly evolves may be restrictive. Many factors, such as differing genetic and environmental backgrounds and many-to-one mapping of form to function, contribute to variability in responses to selection. Nevertheless, lineages may evolve similar, even if not identical, forms given a shared selective regime, providing opportunities to examine the relative importance of natural selection, constraint, and contingency. Here, we show that following 10 transitions to durophagy (eating hard-shelled prey) in moray eels (Muraenidae), cranial morphology repeatedly evolved toward a novel region of morphological space indicative of enhanced feeding performance on hard prey. Disparity among the resulting 15 durophagous species, however, is greater than disparity among ancestors that fed on large evasive prey, contradicting the pattern expected under convergence. This elevated disparity is a consequence of lineage-specific responses to durophagy, in which independent transitions vary in the suites of traits exhibiting the largest changes. Our results reveal a pattern of imperfect convergence, which suggests shared selection may actually promote diversification because lineages often differ in their phenotypic responses to similar selective demands.

Threatened and endangered subspecies with vulnerable ecological traits also have high susceptibility to sea level rise and habitat fragmentation.

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success.

Molecular phylogenetics of moray eels (Muraenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena, Echidna) and multiple colonizations of the Atlantic Ocean.

Moray eels (Muraenidae) are apex predators on coral reefs around the world, but they are not well studied because their cryptic habitats and occasionally aggressive behaviors make them difficult to collect. We provide a molecular phylogeny of moray eels including 44 species representing two subfamilies, eight genera, and all tropical ocean basins. Phylogenetic relationships among these taxa are estimated from portions of mitochondrial loci cytochrome b (632 bp) and cytochrome oxidase subunit 1 (596 bp), and portions of the nuclear loci RAG-1 (421 bp) and RAG-2 (754 bp). We test four sets of contrasting phylogenetic hypotheses using Bayes Factors, Shimodaira-Hasegawa tests, and Templeton tests. First, our results support the subfamily-level taxonomic distinction between true morays (Muraeninae) and snakemorays (Uropterygiinae), statistically rejecting hypotheses of non-monophyly for each subfamily. Second, we reject a monophyletic grouping of the genera Gymnomuraena and Echidna, which share a durophagous (shell-crushing) cranial morphology and dentition, indicating that the durophagous characters are not homologous. Third, we demonstrate that durophagous feeding habits and associated morphological characters have evolved in parallel in an ancestor of Gymnomuraena and at least three additional times within the genus Echidna. Finally, the tree topology indicates multiple invasions of the Atlantic from the Indo-Pacific, one of these occurring immediately prior to formation of the Isthmus of Panama approximately 2.8 MYA (million years ago) and one or two others occurring in the early to mid Miocene. Cladogenesis occurring within the Atlantic during the mid Miocene and Pliocene also contributed to moray species diversity. These data include a pair of sister species separated by the Isthmus of Panama, allowing a time-calibrated tree with an estimated crown age for Muraenidae at between 41 and 60 MYA, consistent with fossil evidence. Most lineage accumulation within morays occurred from the late Oligocene (24-27 MYA) through the Miocene (5-23 MYA) to the late Pliocene (∼ 2.5 MYA).

Phylogeography of two moray eels indicates high dispersal throughout the indo-pacific.

Reef fishes disperse primarily as oceanic "pelagic" larvae, and debate continues over the extent of this dispersal, with recent evidence for geographically restricted (closed) populations in some species. In contrast, moray eels have the longest pelagic larval stages among reef fishes, possibly providing opportunities to disperse over great distances. We test this prediction by measuring mitochondrial DNA (mtDNA) and nuclear DNA variation in 2 species of moray eels, Gymnothorax undulatus (N = 165) and G. flavimarginatus (N = 124), sampled at 14-15 locations across the Indo-Pacific. The mtDNA data comprise 632 bp of cytochrome b and 596 bp of cytochrome oxidase I. Nuclear markers include 2 recombination-activating loci (421 bp of RAG-1 and 754 bp of RAG-2). Analyses of molecular variance and Mantel tests indicate little or no genetic differentiation, and no isolation by distance, across 22 000 km of the Indo-Pacific. We estimate that mitochondrial genetic variation coalesces within the past about 2.3 million years (My) for G. flavimarginatus and within the past about 5.9 My for G. undulatus. Permutation tests of geographic distance on the mitochondrial haplotype networks indicate recent range expansions for some younger haplotypes (estimated within approximately 600 000 years) and episodic fragmentation of populations at times of low sea level. Our results support the predictions that the extended larval durations of moray eels enable ocean-wide genetic continuity of populations. This is the first phylogeographic survey of the moray eels, and morays are the first reef fishes known to be genetically homogeneous across the entire Indo-Pacific.