Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

Abstract The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

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Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda

10.1101/607960 ◽

2019 ◽

Author(s):

Dong Zhang ◽

Hong Zou ◽

Cong-Jie Hua ◽

Wen-Xiang Li ◽

Shahid Mahboob ◽

...

Keyword(s):

Life Histories ◽

Phylogenetic Reconstruction ◽

Mitochondrial Genomes ◽

Origin Of Replication ◽

Long Branch Attraction ◽

Mitochondrial Data ◽

Gc Skew ◽

Limited Applicability ◽

Phylogenetic Hypotheses ◽

Almost All

AbstractThe phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different datasets often producing starkly incongruent phylogenetic hypotheses. We hypothesised that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different datasets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artefacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artefacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements can produce major compositional biases even on short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

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Phylogenetic Reconstruction Based on Synteny Block and Gene Adjacencies

Molecular Biology and Evolution ◽

10.1093/molbev/msaa114 ◽

2020 ◽

Vol 37 (9) ◽

pp. 2747-2762 ◽

Cited By ~ 4

Author(s):

Guénola Drillon ◽

Raphaël Champeimont ◽

Francesco Oteri ◽

Gilles Fischer ◽

Alessandra Carbone

Keyword(s):

Chromosomal Rearrangements ◽

Phylogenetic Reconstruction ◽

Simulated Data ◽

Synteny Block ◽

Data Sets ◽

Reconstruction Method ◽

Reconstruction Methods ◽

Wide Range ◽

Genomic Markers ◽

Almost All

Abstract Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences. PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively, supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches. PhyChro performance is evaluated on two data sets of 13 vertebrates and 21 yeast genomes by using up to 130,000 and 179,000 breakpoints, respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared with other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in <15 min.

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

10.1101/2020.05.09.085712 ◽

2020 ◽

Author(s):

Dong Zhang ◽

Hong Zou ◽

Jin Zhang ◽

Gui-Tang Wang ◽

Ivan Jakovlić

Keyword(s):

Evolutionary History ◽

Phylogenetic Analyses ◽

Branch Length ◽

Mitochondrial Genomes ◽

Close Attention ◽

Mtdna Sequences ◽

Mitochondrial Data ◽

Gc Skew ◽

History Of ◽

Taxonomic Approach

AbstractInversions 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.

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Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life

Molecular Biology and Evolution ◽

10.1093/molbev/msaa251 ◽

2020 ◽

Author(s):

Siddharth Kulkarni ◽

Robert J Kallal ◽

Hannah Wood ◽

Dimitar Dimitrov ◽

Gonzalo Giribet ◽

...

Keyword(s):

Amino Acids ◽

Phylogenetic Signal ◽

Phylogenetic Reconstruction ◽

Data Sets ◽

Noncoding Regions ◽

Nucleotide Data ◽

Codon Positions ◽

Phylogenetic Hypotheses ◽

The Stability ◽

Scale Data

Abstract Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), noncoding regions (included in ultraconserved elements [UCE] analyses), and a combination of both (as in UCE analyses). Gene orthologs, coded as amino acids and nucleotides (with and without third codon positions), were generated by querying published transcriptomes for UCEs, recovering 1,931 UCE loci (codingUCEs). We expected that congeners represented in the codingUCE and UCEs data would form clades in the presence of phylogenetic signal. Noncoding regions derived from UCE sequences were recovered to test the stability of relationships. Phylogenetic relationships resulting from all analyses were largely congruent. All nucleotide data sets from transcriptomes, UCEs, or a combination of both recovered similar topologies in contrast with results from transcriptomes analyzed as amino acids. Most relationships inferred from low-occupancy data sets, containing several hundreds of loci, were congruent across Araneae, as opposed to high occupancy data matrices with fewer loci, which showed more variation. Furthermore, we found that low-occupancy data sets analyzed as nucleotides (as is typical of UCE data sets) can result in more congruent relationships than high occupancy data sets analyzed as amino acids (as in phylotranscriptomics). Thus, omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.

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Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae)

PeerJ ◽

10.7717/peerj.5573 ◽

2018 ◽

Vol 6 ◽

pp. e5573 ◽

Cited By ~ 6

Author(s):

Artur Burzyński ◽

Marianna Soroka

Keyword(s):

Evolutionary Dynamics ◽

Phylogenetic Reconstruction ◽

Real Problem ◽

Data Sets ◽

Long Branch Attraction ◽

The Family ◽

Complete Sequences ◽

First Time ◽

Unio Pictorum ◽

Sinanodonta Woodiana

Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.

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The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory

Genetics ◽

10.1093/genetics/153.1.497 ◽

1999 ◽

Vol 153 (1) ◽

pp. 497-506 ◽

Cited By ~ 4

Author(s):

Rasmus Nielsen ◽

Daniel M Weinreich

Keyword(s):

Dna Sequences ◽

Purifying Selection ◽

Data Sets ◽

Deleterious Mutations ◽

Synonymous Mutations ◽

Weak Evidence ◽

Mitochondrial Data ◽

The Mean ◽

Excess Number ◽

Neutral Mutations

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

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AANMF: Attribute-Aware Attentional Neural Matrix Factorization

Information Technology And Control ◽

10.5755/j01.itc.48.4.23149 ◽

2019 ◽

Vol 48 (4) ◽

pp. 682-693

Author(s):

Bo Zheng ◽

Jinsong Hu

Keyword(s):

Matrix Factorization ◽

Recommendation System ◽

Auxiliary Information ◽

Inner Product ◽

Data Sets ◽

It Projects ◽

Real World Data ◽

Latent Space ◽

Almost All ◽

Novel Model

Matrix Factorization (MF) is one of the most intuitive and effective methods in the Recommendation System domain. It projects sparse (user, item) interactions into dense feature products which endues strong generality to the MF model. To leverage this interaction, recent works use auxiliary information of users and items. Despite effectiveness, irrationality still exists among these methods, since almost all of them simply add the feature of auxiliary information in dense latent space to the feature of the user or item. In this work, we propose a novel model named AANMF, short for Attribute-aware Attentional Neural Matrix Factorization. AANMF combines two main parts, namely, neural-network-based factorization architecture for modeling inner product and attention-mechanism-based attribute processing cell for attribute handling. Extensive experiments on two real-world data sets demonstrate the robust and stronger performance of our model. Notably, we show that our model can deal with the attributes of user or item more reasonably. Our implementation of AANMF is publicly available at https://github.com/Holy-Shine/AANMF.

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Age determination of common bottlenose dolphins (Tursiops truncatus) using dental radiography pulp:tooth area ratio measurements

PLoS ONE ◽

10.1371/journal.pone.0242273 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242273

Author(s):

Jean M. Herrman ◽

Jeanine S. Morey ◽

Ryan Takeshita ◽

Sylvain De Guise ◽

Randall S. Wells ◽

...

Keyword(s):

Life Histories ◽

Marine Mammals ◽

Bottlenose Dolphins ◽

Age Determination ◽

Area Ratio ◽

Dental Radiography ◽

Ratio Method ◽

Data Sets ◽

Photo Identification ◽

Development And Validation

Age is an important parameter to better understand wildlife populations, and is especially relevant for interpreting data for fecundity, health, and survival assessments. Estimating ages for marine mammals presents a particular challenge due to the environment they inhabit: accessibility is limited and, when temporarily restrained for assessment, the window of opportunity for data collection is relatively short. For wild dolphins, researchers have described a variety of age-determination techniques, but the gold-standard relies upon photo-identification to establish individual observational life histories from birth. However, there are few populations with such long-term data sets, therefore alternative techniques for age estimation are required for individual animals without a known birth period. While there are a variety of methods to estimate ages, each involves some combination of drawbacks, including a lack of precision across all ages, weeks-to-months of analysis time, logistical concerns for field applications, and/or novel techniques still in early development and validation. Here, we describe a non-invasive field technique to determine the age of small cetaceans using periapical dental radiography and subsequent measurement of pulp:tooth area ratios. The technique has been successfully applied for bottlenose dolphins briefly restrained during capture-release heath assessments in various locations in the Gulf of Mexico. Based on our comparisons of dental radiography data to life history ages, the pulp:tooth area ratio method can reliably provide same-day estimates for ages of dolphins up to about 10 years old.

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Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development

Molecular Biology and Evolution ◽

10.1093/molbev/msz065 ◽

2019 ◽

Vol 36 (7) ◽

pp. 1373-1383 ◽

Cited By ~ 1

Author(s):

Longjun Wu ◽

Kailey E Ferger ◽

J David Lambert

Keyword(s):

Gene Expression ◽

Large Fraction ◽

Molecular Data ◽

Development Stage ◽

Data Sets ◽

Rna Seq ◽

Developmental Evolution ◽

Phylotypic Stage ◽

Hourglass Model ◽

Almost All

Abstract It has been proposed that animals have a pattern of developmental evolution resembling an hourglass because the most conserved development stage—often called the phylotypic stage—is always in midembryonic development. Although the topic has been debated for decades, recent studies using molecular data such as RNA-seq gene expression data sets have largely supported the existence of periods of relative evolutionary conservation in middevelopment, consistent with the phylotypic stage and the hourglass concepts. However, so far this approach has only been applied to a limited number of taxa across the tree of life. Here, using established phylotranscriptomic approaches, we found a surprising reverse hourglass pattern in two molluscs and a polychaete annelid, representatives of the Spiralia, an understudied group that contains a large fraction of metazoan body plan diversity. These results suggest that spiralians have a divergent midembryonic stage, with more conserved early and late development, which is the inverse of the pattern seen in almost all other organisms where these phylotranscriptomic approaches have been reported. We discuss our findings in light of proposed reasons for the phylotypic stage and hourglass model in other systems.

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Study on the spatial-temporal variation in evapotranspiration in China from 1948 to 2018

Scientific Reports ◽

10.1038/s41598-020-74384-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Feng Zhang ◽

Mengqing Geng ◽

Qiulan Wu ◽

Yong Liang

Keyword(s):

Spatial Variation ◽

Temporal Variation ◽

Basic Research ◽

Variation Coefficient ◽

Data Sets ◽

The North ◽

Mk Test ◽

Increasing Trend ◽

Land Data Assimilation System ◽

Almost All

Abstract It is of great significance for the efficient utilization of water resources and the construction of the ecological environment in China to fully understand the evolution process of the spatial-temporal pattern of evapotranspiration (ET). With the use of the v2.0 and v2.1 ET data sets combined with the Global Land Data Assimilation System and Noah model, this paper selects pixels as the basic research object to analyse the spatial-temporal variation in ET in China during the 71 years from 1948 to 2018. We first applied the TFPW-MK test to study the annual ET trend in China throughout the 71-year period, including the ET trend of each month from January to December and the annual total ET trend. Moreover, we examined the spatial variation in these trends. In addition, we calculated the variation coefficient of the time series of each pixel’s ET throughout the 71-year period and the variation coefficient of the spatial distribution of ET in each year to analyse the spatial-temporal fluctuations in ET in the study area. Finally, the Hurst index was adopted to evaluate the future ET trend. Based on these analyses, we observed the following novel spatial-temporal characteristics of ET: from 1948 to 2018, (1) the ET in most regions covered by 89.5% of all pixels in China exhibits an increasing trend. (2) The ET trend in China varies greatly with the change in months, and many regions show the most or least obvious increasing trend (or decreasing trend) at different times. (3) The area with an increasing trend is the largest in May and the smallest in December, and more than half of the pixels in all months of a year reveal an increasing trend. (4) In the northeast, west and south regions of China, the monthly fluctuation in the ET trend is relatively large, which indicates that the ET trend in these regions is greatly affected by the month. (5) The fluctuation in ET in China is larger in the north than it is in the south and larger in the west than it is in the east. The most stable fluctuation occurs in East China. (6) The ET trend of almost all the pixels in the study area remains consistent from 1948 to 2018, and there are large areas with a notable continuity. This results in the spatial variation in ET in the study area increasing.

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