Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments.

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting.

Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, we introduce bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal is one of the first analysis tools to identify multiple Salmonella enterica serotypes from metagenomic or quasi-metagenomic datasets with high accuracy, allowing these isolate-independent methods to be incorporated into surveillance and root cause investigations. It was tested on an in silico benchmark dataset comprising 29 unique Salmonella serovars, 46 non-Salmonella bacterial genomes, and 10 viral genomes at varying read depths and on previously well-characterized and sequenced non-selective primary and selective enrichments of papaya and peach samples from separate outbreak investigations that resulted in the identification of multiple Salmonella serovars using traditional isolate culturing and WGS as well as nucleic acid assays. Analyses were also conducted on these datasets using a custom-built k-mer tool, SeqSero2, and Kallisto to compare serotype calling to bettercallsal. The in silico dataset analyzed with bettercallsal achieved the maximum precision, recall, and accuracy of 100, 83, and 94%, respectively. In the papaya outbreak samples, bettercallsal identified the presence of multiple serovars in agreement with the Luminex® xMAP assay results and also identified more serovars per sample, as evidenced by NCBI SNP clustering. In peach outbreak samples, bettercallsal identified two serovars in concordance with k-mer analysis and the Luminex xMAP assay. The genome hit reported by bettercallsal clustered with the chicken isolate genome, as reported by the FDA peach outbreak investigation from sequenced isolates (WGS). Overall, bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.

Using low-coverage whole genome sequencing (genome skimming) to delineate three introgressed species of buffalofish (Ictiobus).

Consumption of buffalofish has been sporadically associated with Haff disease-like illnesses involving sudden onset muscle pain and weakness due to skeletal muscle rhabdomyolysis, but determination of precisely which species are associated with these illnesses has been impeded by a lack of species-specific DNA-based markers. Here, three closely related species of buffalofish native to the Mississippi River Basin (Ictiobus bubalus, Ictiobus cyprinellus and Ictiobus niger) that have previously proven genetically indistinguishable using both mitochondrial and nuclear single-locus sequencing were reliably discriminated using low-coverage whole genome sequencing ('genome skimming'). Using 44 specimens representing the three species collected from the mid/upper (Missouri) and lower (Louisiana) regions of the species' native ranges, the SISRS (Site Identification from Short Read Sequences) bioinformatics pipeline was adapted to (1) identify over 620Mbp of putatively homologous nuclear sequence data and (2) isolate over 140,000 single-nucleotide polymorphisms (SNPs) that supported accurate species delimitation, all without the use of a reference genome or annotation data. These sites were used to classify Ictiobus spp. samples with genome-skim data, along with a larger set (n = 67) where ultraconserved elements (UCEs) were sequenced. Analyses of whole mitochondrial data revealed more limited signal. Nearly all samples matched their purported species based on morphologic identification, but two Missouri samples morphologically identified as I. niger grouped with samples of I. bubalus, albeit with significant enrichment of I. niger SNPs. To our knowledge this is the first report of a DNA-based tool to reliably discriminate these three morphologically distinct species.

Validation of the ghost shrimp species Neocallichirus pinheiroi Hernáez, Windsor, Paula amp; Santana (Decapoda: Callianassidae) from the southwestern Atlantic.

Hernáez et al. (2020) described a new species of ghost shrimp, Neocallichirus pinheiroi, from northeastern coast of Brazil, Western Atlantic. Although the description and figures presented by Hernáez et al. (2020) fully characterize the new species, the journal issue in which the description appeared was published online only, and the article in which N. pinheiroi appeared did not include a ZooBank registration number (LISD), required for validation of new names in electronic-only publications [vide Art. 8.5.3 of the amended Code of the International Commission on Zoological Nomenclature (ICZN, 1999, 2012)]. As result, the name Neocallichirus pinheiroi Hernáez, Windsor, Paula Santana, 2020, is not available according the International Code of Zoological Nomenclature (ICZN, 1999, 2012). Therefore, the present note serves to validate the name Neocallichirus pinheiroi by fulfilling the ICZN conditions for nomenclatural availability.

Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin.

Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as "blue crab" and "Product of the USA" may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as "Product of the USA" and "Product of Venezuela." In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise F st values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.

Full Chloroplast Genome Sequence of the Economically Important Dietary Supplement and Spice Curcuma longa.

Curcuma longa L. is a native species of Asia that is commonly known as turmeric. It is a spice also used in traditional medicine to treat a wide range of illnesses. Here, we present the fully annotated chloroplast genome of Curcuma longa.

Resolution of the Portunusgladiator species complex: taxonomic status and identity of Monomiagladiator (Fabricius, 1798) and Monomiahaanii (Stimpson, 1858) (Brachyura, Decapoda, Portunidae).

The United States Food and Drug Administration (FDA) has recently adopted DNA barcoding for the purpose of determining the species identity of commercial seafood products. This effort has revealed instances of incongruence between current scientifically accepted taxon names and those utilized by the seafood industry in product labelling. One such case is that of "Portunushaanii", a name utilized by the seafood industry to label commercial products under the market name "red swimming crab." However, carcinologists currently regard P.haanii as synonym of Portunusgladiator Fabricius, 1798, which itself is the subject of debate over whether it is a secondary homonym of Cancer gladiator Fabricius, 1793. Further complicating matters, DNA barcode sequences from commercial products match GenBank sequences identified as Portunuspseudoargentatus Stephenson, 1961. Here the complicated taxonomic history of the Portunusgladiator complex is reviewed and a resolution proposed based on combined morphological descriptions and molecular phylogenetic analyses. It is demonstrated that, given the provisions of the International Code of Zoological Nomenclature and the current elevation of Monomia Gistel, 1848, to full genus rank, its type species, Portunusgladiator Fabricius, 1798, should be treated as a valid and available taxon name. It is also shown, upon examination and comparison of types and topotypic material that Monomiahaanii (Stimpson, 1858) is a distinct taxon from M.gladiator, and Portunuspseudoargentatus Stephenson, 1961, is a junior subjective synonym of M.haanii (Stimpson, 1858). Furthermore, it is shown that crab meat sold in the US currently labeled as "Portunushaanii" and/or "red swimming crab" is in fact M.haanii using comparative analysis of DNA barcode sequences between museum-vouchered reference specimens, whole crabs provided directly by a seafood importer, and processed commercial products purchased at retail.

The complete mitochondrial genome of Cerion uva uva (Gastropoda: Panpulmonata: Stylommatophora: Cerionidae).

We report the complete mitochondrial genome sequence of Cerion uva uva (Linnaeus 1758), the type species of the type genus of the family Cerionidae. The mitogenome is 15,043 bp in length, has a base composition of A (28.3%), T (34.4%), C (17.3%) and G (20.0%), and contains 13 protein-coding genes, 2 ribosomal RNA genes, as well as 22 transfer RNA genes. Gene order is the same as in Cerion incanum (Leidy 1851), but differs from those of all other Panpulmonata. This is the second mitochondrial genome sequenced within the family Cerionidae and will contribute to the assessment of the phylogeography of this family throughout the islands of the tropical western Atlantic.