Ghost lineages invalidate or reverse several results on gene flow

Introgression, endosymbiosis and gene transfer, i.e. Horizontal Gene Flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection, and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data re-analysis, that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.

Automated Landmarking via Multiple Templates

Geometric morphometrics based on landmark data has been increasingly used in biomedical and biological researchers for quantifying complex phenotypes. However, manual landmarking can be laborious and subject to intra and interobserver errors. This has motivated the development of automated landmarking methods. We have recently introduced ALPACA (Automated Landmarking through Point cloud Alignment and Correspondence), a fast method to automatically annotate landmarks via use of a landmark template as part of the SlicerMorph toolkit. Yet, using a single template may not consistently perform well for large study samples, especially when the sample consists of specimen with highly variable morphology, as it is common evolutionary studies. In this study, we introduce a variation on our ALPACA pipeline that supports multiple specimen templates, which we call MALPACA. We show that MALPACA outperforms ALPACA consistently by testing on two different datasets. We also introduce a method of choosing the templates that can be used in conjunction with MALPACA, when no prior information is available. This K-means method uses an approximation of the total morphological variation in the dataset to suggest samples within the population to be used as landmark templates. While we advise investigators to pay careful attention to the template selection process in any of the template-based automated landmarking approaches, our analyses show that the introduced K-means based method of templates selection is better than randomly choosing the templates. In summary, MALPACA can accommodate larger morphological disparity commonly found in evolutionary studies with performance comparable to human observer.

Phylogenetic Distribution of CRISPR-Cas Systems in Staphylococcus lugdunensis

CRISPR-Cas systems have been characterized as playing several biological roles in many bacterial genomes. Moreover, CRISPR-Cas systems are useful for epidemiological, diagnostic, and evolutionary studies of pathogenic bacteria.

Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India

Oxycarenus laetus is a seed-sap sucking pest affecting a variety of crops, including cotton plants. Rising incidence and pesticide resistance by O. laetus have been reported from India and neighbouring countries. In this study, O. laetus samples were collected from Bhatinda and Coimbatore (India). Pure mtDNA was isolated and sequenced using Illumina MiSeq. Both the samples were found to be identical species (99.9%), and the complete genome was circular (15,672 bp), consisting of 13 PCGs, 2 rRNA, 23 tRNA genes, and a 962 bp control region. The mitogenome is 74.1% AT-rich, 0.11 AT, and − 0.19 GC skewed. All the genes had ATN as the start codon except cox1 (TTG), and an additional trnT was predicted. Nearly all tRNAs folded into the clover-leaf structure, except trnS1 and trnV. The intergenic space between trnH and nad4, considered as a synapomorphy of Lygaeoidea, was displaced. Two 5 bp motifs AATGA and ACCTA, two tandem repeats, and a few microsatellite sequences, were also found. The phylogenetic tree was constructed using 36 mitogenomes from 7 super-families of Hemiptera by employing rigorous bootstrapping and ML. Ours is the first study to sequence the complete mitogenome of O. laetus or any Oxycarenus species. The findings from this study would further help in the evolutionary studies of Lygaeidae.

The red-beard evolutionary explanation of human sociality

Recent evolutionary studies on cooperation devote specific attention to non-verbal expressions of emotions. In this paper, I examine Robert Frank’s popular attempt to explain emotions, non-verbal markers and social behaviours. Following this line of work, I focus on the green-beard explanation of social behaviours. In response to the criticisms raised against this controversial ultimate explanation, based on resources found in Frank’s work, I propose an alternative red-beard explanation of human sociality. The red-beard explanation explains the emergence and evolution of emotions, a proximate cause, rather than patterns of behaviour. In contrast to simple evolutionary models that invoke a green-beard mechanism, I demonstrate that the red-beard explanation can be evolutionary stable. Social emotions are a common cause of a social behaviour and a phenotypic marker and therefore cooperative behaviour cannot be suppressed without also changing the marker.

Echinoderm research perspectives: A Central American bibliometric review

Introduction: Central America, a narrow strip of land dividing the Atlantic and Pacific oceans, has a high diversity of marine and terrestrial species. Echinoderms are one of the most diverse marine groups with 420 reported species. Objective: To summarize echinoderm research in Central America. Methods: We compiled the literature from SCOPUS, Web of Science, SciELO, Google Scholar, Biodiversity Heritage Library, the Internet Archive and the Smithsonian Library. Results: We found 324 publications dating from 1840 to 2020; the early studies had a strong taxonomic focus, but after the 1970s, ecology, evolution and reproduction gained prominence. Echinoidea is the most studied class (38% of publications) due to its use in evolutionary studies as well as the importance of the genus Diadema in reef ecology and dynamics. Conclusion: We recommend more research on fisheries management, conservation and environmental education; and greater integration of local and international research.

Calophyllaceae plastomes, their structure and insights in relationships within the clusioids

A complete chloroplast genome is not yet available for numerous species of plants. Among the groups that lack plastome information is the clusioid clade (Malpighiales), which includes five families: Bonnetiaceae, Calophyllaceae, Clusiaceae, Hypericaceae, and Podostemaceae. With around 2200 species, it has few published plastomes and most of them are from Podostemaceae. Here we assembled and compared six plastomes from members of the clusioids: five from Calophyllaceae (newly sequenced) and one from Clusiaceae. Putative regions for evolutionary studies were identified and the newly assembled chloroplasts were analyzed with other available chloroplasts for the group, focusing on Calophyllaceae. Our results mostly agree with recent studies which found a general conserved structure, except for the two Podostemaceae species that have a large inversion (trnK-UUU–rbcL) and lack one intron from ycf3. Within Calophyllaceae we observed a longer LSC and reduced IRs in Mahurea exstipulata, resulting in some genic rearrangement, and a short inversion (psbJ–psbE) in Kielmeyera coriacea. Phylogenetic analyses recovered the clusioids and the five families as monophyletic and revealed that conflicts in relationships reported in the literature for the group agree with nodes concentrating uninformative or conflicting gene trees. Our study brings new insights about clusioid plastome architecture and its evolution.

HORmon: automated annotation of human centromeres

Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats (HORs)). Even though there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres, and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we demonstrate that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.