Species Delimitation

Species delimitation is the process of determining whether a group of sampled individuals belong to the same species or to different species. The criteria used to delimit species differ across taxonomic groups, and the methods for delimiting species have changed over time, with a dramatic rise in the popularity of genomic approaches recently. Because inferred species boundaries have ramifications that extend beyond systematics, affecting all fields that rely upon species as a foundational unit, controversy has unsurprisingly surrounded not only the practices used to delimit species boundaries, but also the idea of what species are, which varies across taxa (e.g., the use of subspecies varies across the tree of life). This lack of consensus has no doubt contributed to the appeal of genetic-based delimitation. Specifically, genomic data can be collected from any taxon. Moreover, it can be analyzed in a common statistical framework (as popularized by the multispecies coalescent as a model for species delimitation). With the ease of collecting genetic data, the power of genomics, and the purported standardization for diagnosing species limits, genetic-based species delimitation is displacing traditional time-honored (albeit time-consuming) taxonomic practices of species diagnosis. It has also become an invaluable tool for discovering species in understudied groups, and genetic-based approaches are the foundation of international endeavors to generate a catalogue of DNA barcodes to illuminate biodiversity for all of life on the planet. Yet, genomic applications, and especially the sole reliance upon genetic data for inferring species boundaries, are not without their own set of challenges.

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent

Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are “intrinsic,” meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse—albeit indirect—signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.

Description of Aurelia pseudosolida sp. nov. (Scyphozoa, Ulmaridae) from the Adriatic Sea

Until 2021, the genus Aurelia contained eleven described species (WoRMS, 2020), with many genetic species still awaiting a formal description. In 2021, ten new species of Aurelia were described almost solely from genetic data in a novel attempt to use genetic characters as diagnostic characters for species descriptions, leaving seven genetic species still undescribed. Here we present the description of a new Aurelia species from the Adriatic Sea using an integrative taxonomy approach, i.e., employing molecular as well as morphological characteristics in order to describe this new Aurelia species. The species is described based on a single medusa sampled from the town of Rovinj (Croatia), North Adriatic, amidst combined blooms of the ctenophore Mnemiopsis leidy and cnidarian Aurelia solida in the summer of 2020. Based on genetic data, the newly described Aurelia pseudosolida sp. nov. has never been sequenced in any of the previous investigations of the molecular diversity of Aurelia. This is the second species belonging to Discomedusae described from the North Adriatic in little more than half a decade, which could be yet another indication of the susceptibility of the North Adriatic to proliferation of non-indigenous gelatinous species, especially if we take into account historical as well as recent blooms of suspected non-indigenous gelatinous species such as Muggiaea atlantica, Aurelia solida, Mawia benovici and Mnemiopsis leidy.

ABRIDGE: An ultra-compression software for SAM alignment files

Advancement in technology has enabled sequencing machines to produce vast amounts of genetic data, causing an increase in storage demands. Most genomic software utilizes read alignments for several purposes including transcriptome assembly and gene count estimation. Herein we present, ABRIDGE, a state-of-the-art compressor for SAM alignment files offering users both lossless and lossy compression options. This reference-based file compressor achieves the best compression ratio among all compression software ensuring lower space demand and faster file transmission. Central to the software is a novel algorithm that retains non-redundant information. This new approach has allowed ABRIDGE to achieve a compression 16% higher than the second-best compressor for RNA-Seq reads and over 35% for DNA-Seq reads. ABRIDGE also offers users the option to randomly access location without having to decompress the entire file. ABRIDGE is distributed under MIT license and can be obtained from GitHub and docker hub. We anticipate that the user community will adopt ABRIDGE within their existing pipeline encouraging further research in this domain.

First morphometry, reproduction, and genetic data for Blennius ocellaris (Linnaeus, 1758) from the Black Sea

Two specimens of the butterfly blenny, Blennius ocellaris, were caught off the coast of Ordu (Black Sea, Turkey) in April 2021 by trammel net. The aim of this paper is to further document occurrence and distribution of the butterfly blenny for the Black Sea and for Turkish marine ichthyofauna and to provide first morphometric, reproduction, and genetic data on this species to the Black Sea fauna species. Some morphometric and meristic characters were measured and presented as the percentage of total length (TL%). All morphometric measurements except eye diameter, pre-anal length, and maximum body depth were higher in the male individual. It was observed that the head makes up almost 1/4 of the body. It was determined that the ripe eggs were in their final stage of development (Stage IV). Gonad’s weight of a female individual was 2.85 g and the number of eggs was determined as 2993. The mean egg diameter was measured as 1070.7 ±15.63 μm (from 1050.2 to 1123.1 μm). The mitochondrial DNA gene regions of 16S rRNA and COI of the specimens were sequenced and analyzed. The generated partial sequences of COI and 16S rRNA were 621 bp and 551 bp, respectively. The maximum likelihood tree generated with the COI gene sequences retrieved from the GenBank database demonstrated geographic region-based distinction and sequences of the Black Sea specimens nested with the reference specimen sequences from the Western Mediterranean Sea and the Sea of Marmara.

Phylogenetic position of Tropidophorus assamensis Annandale, 1912 with updated morphological data and distributional records

The poorly known northeastern water skink Tropidophorus assamensis is only known from the type locality (Harigaj Range, Sylhet District) in Bangladesh, and few localities in Assam and Mizoram States, north-eastern India. Little is known about the biology including the systematics of the species. In this study, we present for the first time, genetic data (16s rRNA) and inferred its phylogenetic position. In addition to this, we provide updated morphological data along with new distributional records of the species from Mizoram State of north-east India.

Taiwan Biobank: a rich biomedical research database of the Taiwanese population

The Taiwan Biobank (TWB) is an ongoing prospective study of over 150,000 individuals aged 30-70 recruited from across Taiwan beginning in 2012. A comprehensive list of phenotypes was collected for each consented participant at recruitment and follow-up visits through structured interviews and physical measurements. Biomarkers and genetic data were also generated for all participants from blood and urine samples. We present here an overview of the genetic data quality, population structure, and familial relationship within TWB, which consists of predominantly Han Chinese-ancestry individuals, and highlight important attributes and genetic findings thus far from the biobank. A linkage to Taiwan's National Health Insurance database of >25 years and other health-related registries is underway that will enrich the phenotypic spectrum of TWB and enable deep and longitudinal genetic investigations. TWB provides one of the largest biobank resources for biomedical and public health research in East Asia that will contribute to our understanding of the genetic basis of human health and disease in global populations through collaborative studies with other biobanks.