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Fig. 2 in Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation

Fig. 2 The relative synonymous codon usage (RSCU) of Babyrousa babyrussa (a), Cephalorhynchus commersonii (b), Stenella clymene (c), and Stenella frontalis (d). Codon families are plotted on the X axis

Fig. 7 in Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation

Fig. 7 Comparisons of ω values among 34 Cetartiodactyla species of different niches, based on 13 protein-coding genes (PCGs) and each PCG. CL, low-altitude; CM, marine; CH, high-altitude

Fig. 8 in Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation

Fig. 8 Phylogenetic independent contrast analysis between different niches and root-to-tip ω values (Log10-transformed) of 13 PCGs dataset in 34 Cetartiodactyla species

Fig. 5 in Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation

Fig. 5 Estimates of divergence time of Cetartiodactyla species with three fossil calibration points inferred from an analysis of 34 complete mitogenomes

Fig. 1 in Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation

Fig. 1 Gene maps of mitogenome of Babyrousa babyrussa (a), Cephalorhynchus commersonii (b), Stenella clymene (c), and Stenella frontalis (d). The genes outside the circle are transcribed clockwise, while the genes inside are transcribed counterclockwise

Fig. 6 in Divergent evolution of mitogenomics in Cetartiodactyla niche adaptation

Fig. 6 Boxplot of molecular evolution rate (ω) of ND6 gene from 34 Cetartiodactyla species mitogenomes

opennotspecifiedJan 2022View details →

Fig. 2 in Mitogenomics reveals low variation within a trigeneric complex of black corals from the North Pacific Ocean

Fig. 2 Map of collection sites for the specimens in this study including Dendrobathypathes boutillieri USNM-1070762 (circle), Parantipathes cf. larix USNM-1404491 (square), and Lillipathes cf. wingi USNM- 1457355 (triangle)

opennotspecifiedJan 2022View details →

Fig. 1 in Mitogenomics reveals low variation within a trigeneric complex of black corals from the North Pacific Ocean

Fig. 1 Gross morphological comparison of Parantipathes sp. (Museum of Tropical Queens- land G62019; left), Lillipathes sp. (California Academy of Sciences 218816; middle), and Dendrobathypathes sp. (Museo Argentino de Ciencias Naturales-IN 41150; right). These specimens were not analyzed in this study

opennotspecifiedJan 2022View details →

Fig. 4 in Mitogenomics reveals low variation within a trigeneric complex of black corals from the North Pacific Ocean

Fig. 4 Maximum likelihood–based phylogenetic tree based on 13 protein-coding genes and two ribosomal RNAs (29 taxa and 17,651 sites). The tree is rooted internally to the Leiopathidae. Node support

opencc-by-4.0Sep 2024View details →

Supplementary: Comparative mitogenomics provide new insights into phylogeny of Ganoderma

FA files: Supplementary I.15core-genes.cds; Supplementary II.52samples.atp9 & nad4L; Excel files: Supplementary III.Mitogenomes_annotation tables; Supplementary IV.nucleic_acid.stat; Supplementary V. synteny.list

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Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.

opencc-zeroDec 2015View details →

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Data from: Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies

There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ~16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic - including the Mediterranean Sea - and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species.

opencc-zeroDec 2012View details →

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UCE phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders

The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus Batrachuperus, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six Batrachuperus species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern B. karlschmidti population has experienced admixture with B. tibetanus. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of B. pinchonii (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of B. daochengensis and B. yenyuanensis and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.

opencc-zeroJul 2021View details →

Figure 4 in Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne- Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)

Figure 4. Expected (solid line) and observed (broken lines) mismatch distribution of Uropsilus soricipes based on cyt b. The x-axis represents the numbers of pairwise differences among sequences and the y-axis represents the relative frequencies of pairwise comparisons. (A) All individuals; (B) Jiajin Mountains population.

Figure 3. Bayesian 50 in Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne- Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)

Figure 3. Bayesian 50% majority rule consensus phylogenetic tree of Eulipotyphla species from a phylogenetic analysis by the concatenated nucleotide sequences of 12 heavy strand proteincoding genes. Rattus rattus and Tupaia belangeri used as outgroup. The numbers on the internode branche is bootstrap percentages for ML analyses.

Figure 1 in Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne- Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)

Figure 1. Study area and sampling sites for Chinese shrew mole (Uropsilus soricipes) in this study. Sample sizes can be found in Table 1.

Figure 5. Bayesian inference tree using the TIM2 in Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne- Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)

Figure 5. Bayesian inference tree using the TIM2 + I + G model depicting the relationship of Uropsilus soricipes. The phylogenetic tree was rooted using Rattus rattus and Neotetracus sinensis. Numbers represent node supports inferred from Bayesian posterior probabilities. Clade A. Jiajin Mountains (JM); Dujiangyan (DJY); Tianquan (TQ); Maoxian (MX); Lixian (LX); Jiuzhaigou (JZG); Clade B. Yuexi (YX).

opennotspecifiedAug 2021View details →

FIGURE 3 in First record of Seira dowlingi (Wray, 1953) (Collembola, Entomobryidae, Seirinae) from China and mitogenome comparison with the New World specimens

FIGURE 3. Phylogenetic position of the Chinese Seira dowlingi (highlighted in yellow). Red dots are marking the nodes with bootstrap ≥ 99%. Seira species are represented in pink; Tyrannoseira species are represented in green; Lepidocyrtinus species are represented in blue.

opennotspecifiedAug 2021View details →

FIGURE 2 in First record of Seira dowlingi (Wray, 1953) (Collembola, Entomobryidae, Seirinae) from China and mitogenome comparison with the New World specimens

FIGURE 2. Comparative map of mitogenomes in relation to the Brazilian Seira dowlingi (pink ring). Grey ring indicates genes feature annotations. Circles from the outer to inner side represent S. dowlingi (Brazilian specimens), S. dowlingi (Chinese specimens), S. sanloemensis, S. atrolutea, Tyrannoseira bicolorcornuta, Lepidocyrtinus dapeste, Lepidocyrtoides caeruleomaculatus, and Entomobrya proxima, respectively.