Cryptic Torrent Frogs of Myanmar: An Examination of the Amolops marmoratus Species Complex with the Resurrection of Amolops afghanus and the identification of a New Species

Cataloged from PDF version of article.We investigated diversity in the Amolops marmoratus species complex within Myanmar using both molecular and morphological characters from recently collected specimens. Based on congruence between multivariate analyses of quantitative morphological characters and phylogenetic analyses of nucleotide variation in the 16S ribosomal gene conducted on 43 out of 182 frogs examined, we recognize A. marmoratus for specimens from the states of Mon and Shan and northern Tanintharyi Division and designate a neotype for this species; resurrect A. afghanus (Gnther, 1858) from synonymy with A. marmoratus for specimens from the northern state of Kachin and designate a lectotype for this species; recognize A. panhai for specimens from Tanintharyi, a new country record; and describe a new species for specimens from the western states of Chin and Rakhine, and Sagaing Division. © 2012 by the American Society of Ichthyologists and Herpetologists

Genotypes file for genetic map

This file is the input data file used for map construction in joinmap format (.loc) produced by the program Stacks 1.3.5 assuming a cp cross design. The first column gives the locus ID assigned to each marker by the program Stacks 1.3.5. The next column gives the segregation type code for each marker using the joinmap 4 convention. Each subsequent column provides the genotypes for an individual for all 9029 markers. Missing data is coded as “--“. The ID for each individual is given as a list in the first column underneath the last locus ID

Genome-wide variant calls

This file contains the genome-wide variant calls (SNPs) for all 37 individuals included in the study. Variants were called with GATK v3.8 using UnifiedGenotyper and following the best practices work flow

Genome-wide VCF including invariant sites

This VCF file includes genotype calls for all 37 individuals included in the study at both variant and invariant sites. This file was generated using GATK v3.8 UnifiedGenotyper by including the EMIT_ALL_SITES option, and was used to more accurately estimate dxy and nucleotide diversity in genomic windows

Genetic map

This file contains the full genetic map used to estimate recombination rates and scaffold the genome. ‘LG’ is the linkage group identifier, which ranges from 1 – 10. The stacks_id field contains the locus ID allocated to each marker by the program Stacks 1.3.5 (Catchen et al. 2013). bp is the base-pair position of the marker within the M. aurantiacus assembly at the chromosome scale. Contig is the assembly contig (scaffold) that each marker is associated with. cM gives the sex-averaged map position estimated for each marker

Genome-wide data in nonoverlapping 100kb windows

This file includes population genetic statistics, measures of genomic features, and estimates of phylogenetic concordance in 100kb nonoverlapping windows across the bush monkeyflower genome, which were used in analyses of genomic landscape evolution. Fst and dxy are included for 36 pairwise comparisons between taxa, and nucleotide diversity is included for all 9 taxa. These statistics were calculated using python scripts downloaded from https://github.com/simonhmartin/genomics_general. PC1 Fst, PC1 dxy, and PC1 nucleotide diversity for each window are obtained by performing a PCA using the 36 comparisons (fst or dxy) or 9 taxa (nucleotide diversity) as variables, and provide a summary of variation across taxa or taxon comparisons in each of these statistics. Gene count is obtained from the genome annotation, recombination rate (cM/Mb) is based on the genetic map, and tree concordance is obtained by taking the correlation coefficient between the window based tree and the whole genome ‘species tree.

Genome-wide data in nonoverlapping 500kb windows

This file includes population genetic statistics, measures of genomic features, and estimates of phylogenetic concordance in 500kb nonoverlapping windows across the bush monkeyflower genome, which were used in analyses of genomic landscape evolution. Fst and dxy are included for 36 pairwise comparisons between taxa, and nucleotide diversity is included for all 9 taxa. These statistics were calculated using python scripts downloaded from https://github.com/simonhmartin/genomics_general. PC1 Fst, PC1 dxy, and PC1 nucleotide diversity for each window are obtained by performing a PCA using the 36 comparisons (fst or dxy) or 9 taxa (nucleotide diversity) as variables, and provide a summary of variation across taxa or taxon comparisons in each of these statistics. Gene count is obtained from the genome annotation, recombination rate (cM/Mb) is based on the genetic map, and tree concordance is obtained by taking the correlation coefficient between the window based tree and the whole genome ‘species tree.

Tree topologies in 500kb non-overlapping windows

This file contains ML trees estimated by RAxML using MVFtools in 500kb non-overlapping windows. These were used to calculate the estimate of tree concordance based on the correlation with the species tree topology

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers.

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic "landscape" of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the 9 taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (BGS; i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation

The genome of the Gulf pipefish enables understanding of evolutionary innovations

BACKGROUND: Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. RESULTS: We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. CONCLUSIONS: The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1126-6) contains supplementary material, which is available to authorized users