The forest for the trees: evaluating molecular phylogenies with an emphasis on higher-level Decapoda

Zou

et al. 2020

Preprint

Inversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. The number of ORI events in crustaceans remains unknown; several studies reported ORI events in some crustacean lineages on the basis of fully inversed (e.g. negative vs. positive) GC skew patterns, but studies of isolated lineages could have easily overlooked ORI events that produced merely a reduction in the skew magnitude. In this study, we used a comprehensive taxonomic approach to systematically study the evolutionary history of ORI events in crustaceans using all available mitogenomes and combining signals from lineage-specific skew magnitude and direction (+ or -), cumulative skew diagrams, and gene rearrangements.We inferred 24 putative ORI events (14 of which have not been proposed before): 17 with relative confidence, and 7 speculative. Most of these were located at lower taxonomic levels, but there are indications of ORIs that occurred at or above the order-level: Copepoda, Isopoda, and putatively in Branchiopoda and Poecilostomatida+Cyclopoida. Several putative ORI events did not result in fully inversed skews. In many lineages skew plots were not informative for the prediction of replication origin and direction of mutational pressures, but inversions of the mitogenome fragment comprising the ancestral CR (rrnS-CR-trnI) were rather good predictors of skew inversions. We also found that skew plots can be a useful tool to indirectly infer the relative strengths of mutational/purifying pressures in some crustacean lineages: when purifying pressures outweigh mutational, GC skew plots are strongly affected by the strand distribution of genes, and when mutational > purifying, GC skew plots can be even completely (apparently) unaffected by the strand distribution of genes. This observation has very important repercussions for phylogenetic and evolutionary studies, as it implies that not only the relatively rare ORI events, but also much more common gene strand switches and same-strand rearrangements can produce mutational bursts, which in turn affect phylogenetic and evolutionary analyses. We argue that such compositional biases may produce misleading signals not only in phylogenetic but also in other types of evolutionary analyses (dN/dS ratios, codon usage bias, base composition, branch length comparison, etc.), and discuss several such examples. Therefore, all studies aiming to study the evolution of mtDNA sequences should pay close attention to architectural rearrangements.

Section: No Class Subclass Order Suborder/family Genus/species Gc Cosupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes

Zou

et al. 2020

Preprint

“…13). Decapod monophyly is established by phylogenetic analysis of protein-coding genes (Bracken et al, 2009;Bybee et al, 2011;Timm and Bracken-Grissom, 2015), morphology (Legg et al, 2013;Richter and Scholtz, 2001), and combined morphology and molecular data ). Analyses of whole mitochondrial genomes place Euphausiacea (krill) within Decapoda (Shen et al, 2015), a result congruent with acquisition of a nauplius larval stage (though this is accepted as convergent: (Jirikowski et al, 2013;Scholtz, 2000).…”

Section: Crown Decapodamentioning

confidence: 99%

Fossil Calibrations for the Arthropod Tree of Life

Wolfe

Daley

Legg³

et al. 2016

Preprint

Fossil age data and molecular sequences are increasingly combined to establish a timescale for the Tree of Life. Arthropods, as the most species-rich and morphologically disparate animal phylum, have received substantial attention, particularly with regard to questions such as the timing of habitat shifts (e.g., terrestrialisation), genome evolution (e.g., gene family duplication and functional evolution), origins of novel characters and behaviours (e.g., wings and flight, venom, silk), biogeography, rate of diversification (e.g., Cambrian explosion, insect coevolution with angiosperms, evolution of crab body plans), and the evolution of arthropod microbiomes. We present herein a series of rigorously vetted calibration fossils for arthropod evolutionary history, taking into account recently published guidelines for best practice in fossil calibration. These are restricted to Palaeozoic and Mesozoic fossils, no deeper than ordinal taxonomic level, nonetheless resulting in 79 fossil calibrations for 101 clades. This work is especially timely owing to the rapid growth of molecular sequence data and the fact that many included fossils have been described within the last five years. This contribution provides a resource for systematists and other biologists interested in deep-time questions in arthropod evolution.

“…The data collected during the DEEPEND cruises have enabled various studies to understand the oceanic environments in the northern GoM including remote sensing studies of surface salinity changes (Chen & Hu, 2017); evaluation of atmospheric correction schemes for satellite measurements (Zhang et al, 2018); development of validation criteria for satellite-derived ocean properties (Barnes et al, 2019); the use of glider data to observe vertical migration of Karenia brevis (Hu et al, 2016); the influence of light and oceanographic structuring on acoustically observed deep scattering layer patterns (Boswell et al, 2018); the use of genome-scale ddRADseq methods to elucidate genetic diversity and connectivity patterns, and phylogenetic diversity in cephalopods (Timm et al, 2018b), crustaceans (Robalino et al, 2016;Timm & Bracken-Grissom, 2015;Timm et al, 2018aTimm et al, , 2018c, and fishes; use of molecular genetics to characterize microbial community structures (Easson & Lopez, 2018), which in turn can support the identification of mesoscale oceanographic features ; the use of PAHs to understand bioaccumulation patterns of toxic compounds in deep-pelagic fauna; and use of the HYCOM model to classify and predict physical oceanographic features in the GoM Johnston et al, 2018). Altogether, this work represents substantial progress in understanding how pelagic ecosystems are structured and connected through the GoM across a range of spatial and tem-poral scales, the physical and chemical drivers that most strongly influence the fauna, and improves our understanding of how these ecosystems may be influenced by anthropogenic impacts in the future.…”

Section: Discussionmentioning

confidence: 99%

The Application of Novel Research Technologies by the Deep Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND) Consortium

Milligan¹,

Bernard²,

Boswell³

et al. 2018

mar technol soc j

Self Cite

S table isotope analysis (SIA) is a popular method of delineating food web structure as it provides a view of an organism's diet over time scales relevant to tissue turnover rates rather than digestion rates. Carbon isotopes (δ 13 C) are used to determine the relative contribution of different carbon sources (primary producers) to consumers within a food web, while nitrogen isotopes (δ 15 N) are used to assign consumers to specific trophic positions. However, sampling primary producers in pelagic systems across spatially and temporally comprehensive scales is difficult and expensive.A powerful supplementary approach to traditional SIA is the use of compound-specific SIA of amino acids (CS-SIA AA), which allows for the designation of trophic positions without the collection of primary producers. The CS-SIA AA method works A B S T R A C TThe deep waters of the open ocean represent a major frontier in exploration and scientific understanding. However, modern technological and computational tools are making the deep ocean more accessible than ever before by facilitating increasingly sophisticated studies of deep ocean ecosystems. Here, we describe some of the cutting-edge technologies that have been employed by the Deep Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND; www.deependconsortium.org) Consortium to study the biodiverse fauna and dynamic physical-chemical environment of the offshore Gulf of Mexico (GoM) from 0 to 1,500 m.