Phylogenetic Relationship Among Horseshoe Crab Species: Effect of Substitution Models on Phylogenetic Analyses

As an interface between terrestrial and marine environments, coastal and estuarine areas are particularly prone to various pollution stresses. Identification of sentinel species is, therefore, essential to provide precautionary information on coastal health conditions. Given their significant ecological roles in estuarine ecosystems, horseshoe crabs are a potential species to indicate the general health status of coastal habitats. The present study demonstrated that the changes in haemolymph composition pattern of two Asian juvenile horseshoe crab species (Tachypleus tridentatus and Carcinoscorpius rotundicauda) are sensitive to reflect heavy metal (lead, nickel and iron) and nutrient (nitrate and ammonia) concentrations of intertidal sediments. In particular, a significant negative correlation was found for the amebocyte viability and ratio of granular–spherical to granular–flattened and degranulated dendritic-like morphological states of amebocytes in juvenile haemolymph with nitrate and lead concentrations respectively. There were also significantly higher concentrations of haemolymph haemocyanin and plasma protein in juvenile C. rotundicauda than in T. tridentatus on the same shore, possibly being related to the difference in foraging habitats of these two horseshoe crab species. Such non-lethal sampling of haemolymph from juvenile horseshoe crabs can be useful for a further development of the monitoring program in assessing potential environmental impacts by anthropogenic activities.

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Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

BMC Evolutionary Biology ◽

10.1186/1471-2148-9-119 ◽

2009 ◽

Vol 9 (1) ◽

pp. 119 ◽

Cited By ~ 89

Author(s):

Björn M von Reumont ◽

Karen Meusemann ◽

Nikolaus U Szucsich ◽

Emiliano Dell'Ampio ◽

Vivek Gowri-Shankar ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Background Knowledge ◽

Substitution Models

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Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?

Australian Journal of Zoology ◽

10.1071/zo09049 ◽

2009 ◽

Vol 57 (4) ◽

pp. 167 ◽

Cited By ~ 4

Author(s):

Gavin Huttley

Keyword(s):

Common Ancestor ◽

Phylogenetic Analyses ◽

Sequence Divergence ◽

Protein Coding ◽

Substitution Models ◽

True Tree ◽

Molecular Phylogenetic ◽

Tree Topologies ◽

Mammal Evolution ◽

Genome Projects

Did the mammal radiation arise through initial divergence of prototherians from a common ancestor of metatherians and eutherians, the Theria hypothesis, or of eutherians from a common ancestor of metatherians and prototherians, the Marsupionta hypothesis? Molecular phylogenetic analyses of point substitutions applied to this problem have been contradictory – mtDNA-encoded sequences supported Marsupionta, nuclear-encoded sequences and RY (purine–pyrimidine)-recoded mtDNA supported Theria. The consistency property of maximum likelihood guarantees convergence on the true tree only with longer alignments. Results from analyses of genome datasets should therefore be impervious to choice of outgroup. We assessed whether important hypotheses concerning mammal evolution, including Theria/Marsupionta and the branching order of rodents, carnivorans and primates, are resolved by phylogenetic analyses using ~2.3 megabases of protein-coding sequence from genome projects. In each case, only two tree topologies were being compared and thus inconsistency in resolved topologies can only derive from flawed models of sequence divergence. The results from all substitution models strongly supported Theria. For the eutherian lineages, all models were sensitive to the outgroup. We argue that phylogenetic inference from point substitutions will remain unreliable until substitution models that better match biological mechanisms of sequence divergence have been developed.

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Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Genes ◽

10.3390/genes11010115 ◽

2020 ◽

Vol 11 (1) ◽

pp. 115

Author(s):

Yuxin Hu ◽

Weiyue Xing ◽

Zhengyu Hu ◽

Guoxiang Liu

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Phylogenetic Relationship ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Substitution Rates ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Volvocine Algae

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

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Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence

Frontiers in Plant Science ◽

10.3389/fpls.2020.619799 ◽

2021 ◽

Vol 11 ◽

Author(s):

Jinyuan Chen ◽

Guili Wu ◽

Nawal Shrestha ◽

Shuang Wu ◽

Wei Guo ◽

...

Keyword(s):

Phylogenetic Relationship ◽

Species Delimitation ◽

Large Scale ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Population Based ◽

Integrative Approach ◽

Morphological Evidence ◽

Sampling Errors ◽

Lineage Sorting

Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago, eight Trigonella, and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA, trnK-matK, and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera.

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Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae

10.1101/674333 ◽

2019 ◽

Cited By ~ 3

Author(s):

Adriano de Bernardi Schneider ◽

Denis Jacob Machado ◽

Daniel Janies

Keyword(s):

Phylogenetic Relationship ◽

Soybean Cyst Nematode ◽

Phylogenetic Analyses ◽

Optimality Criteria ◽

Entire Family ◽

Close Phylogenetic Relationship ◽

The Family ◽

Relationship Of ◽

Reference Genomes ◽

Annotation Strategy

The ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and zika, demand a greater understanding of how these viruses evolve, emerge and spread in order to respond. Central to this understanding is an updated phylogeny of the entire family. Unfortunately, most cladograms of Flaviviridae focus on specific lineages, ignore outgroups, and rely on midpoint rooting, hampering their ability to test ingroup monophyly and estimate ingroup relationships. This problem is partly due to the lack of fully annotated genomes of Flaviviridae, which has genera with slightly different gene content, hindering genome analysis without partitioning. To tackle these problems, we developed an annotation pipeline for Flaviviridae that uses a combination of ab initio and homology-based strategies. The pipeline recovered 100% of the genes in reference genomes and annotated over 97% of the expected genes in the remaining non curated sequences. We further demonstrate that the combined analysis of genomes of all genera of Flaviviridae (Flavivirus, Hepacivirus, Pegivirus, and Pestivirus), as made possible by our annotation strategy, enhances the phylogenetic analyses of these viruses for all optimality criteria that we tested (parsimony, maximum likelihood, and posterior probability). The final tree sheds light on the phylogenetic relationship of viruses that are divergent from most Flaviviridae and should be reclassified, especially the soybean cyst nematode virus 5 (SbCNV-5) and the Tamana bat virus. We also corroborate the close phylogenetic relationship of dengue and zika viruses with an unprecedented degree of support.

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