Genetic utility of natural history museum specimens: endangered fairy shrimp (Branchiopoda, Anostraca)

Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets

Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

The first record of Tremoctopus violaceus sensu stricto Delle Chiaje,1830 in southwestern Gulf of Mexico gives a hint of the taxonomic status of Tremoctopus gracilis

Knowledge on species taxonomic identity is essential to understand biological and biogeographical processes and for studies on biodiversity. Species the genus Tremoctopus have been confused in the past and are inconsistently identified. To clarify of the taxonomic diagnosis Tremoctopusviolaceus Delle Chiaje, 1830, an evaluation of morphological and meristic characters, as well as morphometric indices and genetic analyses, was undertaken. The analyzed octopod was an opportunistically collected mature female of 640 mm in total length, with a mantle length of 135 mm and a total weight of 1.02 kg. Evidence of autotomy as a defensive mechanism for protecting the egg mass is presented. The 16S haplotype sequenced from this specimen represents the first one publicly available for this species from the Gulf of Mexico. The genetic divergence between this haplotype and those reported from the Pacific Ocean is representative of interspecific variation in other taxa, which suggests that “T.violaceus” in the Pacific Ocean (KY649286, MN435565, and AJ252767) should be addressed as T.gracilis instead. Genetic evidence to separate T.violaceus and T.gracilis is presented. The studied specimen from the Gulf of Mexico represents the westernmost known occurrence of T.violaceus and the first record from the southwestern Gulf of Mexico.

An integrative taxonomic approach reveals Octopus insularis as the dominant species in the Veracruz Reef System (southwestern Gulf of Mexico)

The common octopus of the Veracruz Reef System (VRS, southwestern Gulf of Mexico) has historically been considered as Octopus vulgaris, and yet, to date, no study including both morphological and genetic data has tested that assumption. To assess this matter, 52 octopuses were sampled in different reefs within the VRS to determine the taxonomic identity of this commercially valuable species using an integrative taxonomic approach through both morphological and genetic analyses. Morphological and genetic data confirmed that the common octopus of the VRS is not O. vulgaris and determined that it is, in fact, the recently described O. insularis. Morphological measurements, counts, indices, and other characteristics such as specific colour patterns, closely matched what had been reported for O. insularis in Brazil. In addition, sequences from cytochrome oxidase I (COI) and 16S ribosomal RNA (r16S) mitochondrial genes confirmed that the common octopus from the VRS is in the same highly supported clade as O. insularis from Brazil. Genetic distances of both mitochondrial genes as well as of cytochrome oxidase subunit III (COIII) and novel nuclear rhodopsin sequences for the species, also confirmed this finding (0-0.8%). We discuss our findings in the light of the recent reports of octopus species misidentifications involving the members of the 'O. vulgaris species complex' and underscore the need for more morphological studies regarding this group to properly address the management of these commercially valuable and similar taxa.

Range-wide phylogeographic structure of the vernal pool fairy shrimp (Branchinecta lynchi)

Wetland habitats across the world are experiencing rapid modification and loss due to accelerating habitat conversion. Impacts to wetland habitats are particularly acute in California where up to 90% of wetland habitats have been modified or lost. Vernal pool ecosystems have therefore undergone a dramatic loss in habitat and along with them an entire endemic fauna is under threat of extinction. Recent efforts to conserve vernal pool habitat and associated species have involved restoration and creation of vernal pools as well as translocations of threatened species. The vernal pool fairy shrimp, Branchinecta lynchi, is one of several endemic and federally listed species being targeted for translocations. To guide reintroduction and conservation, detailed information on range-wide population structure and diversity is needed. We collected genetic data from two mitochondrial genes throughout the known extant range of B. lynchi to elucidate population structure and diversity of the species. We found support for phylogeographic structure throughout the range of B. lynch associated with isolated watersheds and vernal pool regions previously identified in the recovery plan for the species. The underlying mechanisms responsible for this broad pattern of genetic structure have yet to be identified. However, the evidence of only a few haplotypes being shared across the species range and patterns of isolation by distance within vernal pool regions suggests dispersal limitation may play a role. These results stress that conservation programs, at a minimum, should consider using individuals from regional populations as sources for reintroductions to maintain historical patterns of genetic differentiation. Additionally, because genetic structure is associated with vernal pool regions which are based on local hydrology and geology, translocations should proceed considering the distance between donor and recipient sites.

Collecting and preserving marine and freshwater isopoda (crustacea: peracarida)

Background

Isopoda are the most diverse Crustacea. In order to encourage the study of isopod crustaceans and their use in biodiversity studies, systematics, ecology, physiology and more, one needs to know who the isopods are and where to find them.

New information

This is a short “how to” guide focusing on the free-living marine and freshwater isopods: where they live and how to collect and preserve them. The tools and techniques described here are simple, but invaluable in accessing the natural history of these remarkable creatures.