Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

The high‐throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low‐quantity and low‐quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100‐year old museum‐preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample‐specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.     

Description of the first species of Pseudoendorchis (Cestoda: Proteocephalidae) with uniloculate suckers from the pimelodid catfish Megalonema platycephalum,with comments on the taxonomic importance of the terminal vagina

Systematic Parasitology - The proteocephalid genus Pseudoendorchis (Cestoda: Onchoproteocephalidea) has recently been proposed to accommodate seven species/species-level lineages of tapeworm...     

A social panorama within the life cycle thinking and the circular economy: a literature review

Purpose

This literature review aims to present the current methodologies that have been developed to perform a social life cycle assessment (sLCA) and to display the main differences among them. In addition to that, to identify the nexus between sLCA and circular economy (CE) and to what extent this life cycle technique has been involved within CE studies.

Methods

An analysis of scientific literature using online databases was made. A total of 76 publications, including all industry sectors worldwide, were chosen spanning 11 years, from 2009 to 2020. Special attention was made to the methodology used to assess the social impacts, the impact categories analyzed, and whether there is or not a circular economy case. All the impact categories of both UNEP/SETAC and PSIA were taken into account when doing the review, and the top three of the categories are mentioned here.

Results and discussion

The leadership of the UNEP/SETAC methodology is clear with 58 cases. Almost 90% of the case studies are focused on products while the remaining ones are related with services. Workers are the most considered stakeholder when conducting an sLCA research, followed by local communities and society. Regarding the impact assessment, the performance reference point (PRP) was the most common method used. When considering the CE even when some cases included the end-of-life stage in the system boundaries, the studies did not consider the actors from that stage; excluding these cases, one out of four articles has a link with CE, a promising proportion taking into account the early stage of both concepts (i.e., sLCA and CE).

Conclusions

UNEP/SETAC guidelines seem to be the most promising methodology due to its reception among the scientific community. However, a more industry-oriented approach is proposed by the Roundtable for Product Social Metrics (PSIA) in a way to respond to manufacturing companies’ demand. Regardless of the type of methodology to be implemented, workers represent the key stakeholder when assessing social impacts. The change in usual patterns is leading to a change in the way how stakeholders interact and therefore new and more impacts may arise, and that is the reason why it is important to include the CE into the sLCA. A series of challenges such as the feasibility of aggregating all the life cycle techniques to one (life cycle sustainability assessment), data availability, and quality are still present for the moment.

     

Small and overlooked: Phylogeny of the genus Trigonodactylus (Squamata: Gekkonidae), with the first record of Trigonodactylus arabicus from Jordan

Geckos of the genus Trigonodactylus are widely distributed in the sand deserts of the Arabian Peninsula. Three species of this genus are currently recognized, with a fourth one, Stenodactylus pulcher, which placement within Trigonodactylus has been tentatively suggested, but not yet confirmed. We present a phylogenetic analysis of the genus Trigonodactylus with new specimens collected in central Saudi Arabia and southern Jordan. New genetic data has been generated from three mitochondrial markers to investigate the phylogenetic relationships of all species of the genus and to assess the putative generic assignment of S. pulcher. Our results confirm that S. pulcher indeed belongs within Trigonodactylus, branching as a sister lineage to all other species of the genus. The new samples cluster within Trigonodactylus arabicus, thus confirming the genetic homogeneity of the species across its large and seemingly inhospitable range. The new specimen collected in southern Jordan represents the first record for the country and a considerable range extension to the northwest from all previously reported localities. Our findings and discovery of a new species for Jordan highlight the need of more field surveys to be carried out in the underexplored parts of Jordan and northern Saudi Arabia, as these places still hold a potential for new discoveries and are crucial for understating the biogeography of the Arabian herpetofauna.     

A mixed finite element formulation for a non-linear,transversely isotropic material model for the cardiac tissue

In this paper we present a mixed finite element method for modeling the passive properties of the myocardium. The passive properties are described by a non-linear, transversely isotropic, hyperelastic material model, and the myocardium is assumed to be almost incompressible. Single-field, pure displacement-based formulations are known to cause numerical difficulties when applied to incompressible or slightly compressible material cases. This paper presents an alternative approach in the form of a mixed formulation, where a separately interpolated pressure field is introduced as a primary unknown in addition to the displacement field. Moreover, a constraint term is included in the formulation to enforce (almost) incompressibility. Numerical results presented in the paper demonstrate the difficulties related to employing a pure displacement-based method, applying a set of physically relevant material parameter values for the cardiac tissue. The same problems are not experienced for the proposed mixed method. We show that the mixed formulation provides reasonable numerical results for compressible as well as nearly incompressible cases, also in situations of large fiber stretches. There is good agreement between the numerical results and the underlying analytical models.