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Fig. 9 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

Fig. 9. Variation of summarized tv/ts-index in micro- (1) and macromammals (2) depending on nucleotide substitution level. Thick lines illustrate exponential approximation.

Fig. 8 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

Fig. 8. Variation of transition (upper lines) and transversion (lower lines) frequencies accordingly to substitution frequencies level. Think lines are empirical data for each subfamily/family, thick ones — polynomial approximations of averaged data.

Fig. 2 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

Fig. 2. Average frequencies of nucleotide substitutions frequencies (sub) and its standard errors of the three taxonomical levels in micromammals (black) and macromammals (gray).

T a b l e 1 in Cryptic Speciation And Characteristics Of The Transition Bias Following An Example Of The Cytb Gene In Palearctic Mammals

T a b l e 1. Average (M), sample deviations (SD) of nucleotide substitution, ts/tv and F indexes of different taxonomical levels within 15 Palearctic mammal families/subfamilies

figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling

figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95% highest posterior density interval is shown in blue.

figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling

figure 2 The dated phylogenetic trees using the cytb gene for G. subgutturosa. Blue bars show 95% highest posterior density intervals of the estimated node ages; numbers next to the nodes are mean node ages (Mya). The red and green lines show new haplotypes from this study.

opencc-zeroMar 2024View details →

COI and Cytb data of Lagocephalus spadiceus in eight populations

The Late Pleistocene-Holocene climate fluctuations have had a major impact on phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. Lagocephalus spadiceus is a high-nutritional and economic-value species in the Southeast China Sea. The study was to assess the population genetic diversity and demography of L. spadiceus in the South China Sea (SCS). A sample of 300 specimens from eight geographic locations along the coast of mainland China and Hainan Island were obtained for this study. The mitochondrial cytochrome oxidase I (COI) and cytochrome b (Cyt b) gene datasets had high haplotype diversity but low nucleotide diversity. The genetic structure and phylogenetic analyses indicated that there was no significant population structure among the eight geographic locations. The low genetic diversity of L. spadiceus was associated with population expansion in the Late Pleistocene-Holocene period. This was supported by star haplotype networks, neutrality tests, unimodal mismatch distributions and Bayesian skyline plots. These findings have important reference value for the protection of genetic resources. Furthermore, the study illuminates the complex relationship between Pleistocene-Holocene temperature variability and phylogeography.

opencc-zeroOct 2022View details →

Cytb gene sequences of Fejervarya species from Lesser Sunda, Indonesia and other Asian countries

Cyt b gene sequences of Fejervarya species were done and later submitted to DDBJ. Then, we received accession number which are used in our manuscript "Postmating isolation and evolutionary relationships among Fejervarya species from Lesser Sunda, Indonesia and other Asian countries revealed by crossing experiments and mtDNA Cytb sequences analyses". These are genuine data. There is no conflict of interest of these data.

publicMar 2024View details →

COI and Cytb data of Lagocephalus spadiceus in eight populations

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publicOct 2022View details →

Cytb gene sequences of Fejervarya species from Lesser Sunda, Indonesia and other Asian countries

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opennotspecifiedNov 2015View details →

III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences in Description of a new species of the genus Aselliscus (Chiroptera, Hipposideridae) from Vietnam

III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences

opennotspecifiedOct 2020View details →

FIGURE 1. Maximum likelihood tree for cytb and ITS2 in Contributions to Disholcaspis Dalla Torre And Kieffer (Hymenoptera: Cynipidae: Cynipini)

FIGURE 1. Maximum likelihood tree for cytb and ITS2, for known species of Disholcaspis and unidentified specimens. Names starting with "D_" represent specimens from Nicholls et al. (2017). Names starting with USNM are newly collected; those in blue (only) can be assigned to previously-described species based on phylogenetic placement, genetic distances, and host plant data. Bootstrap values above 50% are shown to the left of the nodes.

opennotspecifiedJan 2021View details →

FIGURE 4. Combined haplotype networks from CytB data for Laminatubus paulbrooksi n in Laminatubus (Serpulidae, Annelida) from eastern Pacific hydrothermal vents and methane seeps, with description of two new species

FIGURE 4. Combined haplotype networks from CytB data for Laminatubus paulbrooksi n. sp. (top) from Pacific Costa Rica margin and Gulf of California (Mexico) localities and L. joycebrooksae n. sp. (bottom) from Costa Rica. There was little variability among the L. joycebrooksae n. sp. sequences and a distinct break to L. paulbrooksi n. sp. This corresponds to a minimum 6.4% uncorrected distance. Laminatubus paulbrooksi n. sp. showed marked intraspecific variability with distinct breaks among the three main sites; Costa Rica (9°N), Pescadero (23°N) and Guaymas Basin (27°N). * indicates the holotypes for L. paulbrooksi n. sp. and L. joycebrooksae n. sp. respectively.

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Cytb + ND2 Prinia gracilis complex

Prinias (Cisticolidae: Prinia) are resident warblers of open areas across Africa and Asia and include many polytypic species whose species limits have not been seriously reevaluated recently. Based on an integrative taxonomic analysis of morphology, song, and mitochondrial DNA (mtDNA), we suggest that 2 species should be recognized in the Graceful Prinia (Prinia gracilis) complex. In addition, our morphological analyses show the existence of a well-marked undescribed form in southeastern Somalia, which we name herein as a new subspecies. Prinia gracilis is a small, drab, long-tailed species with streaking above and plain pale underparts that has been suggested to fall into 2 groups: the southwestern nominate group (from Egypt to Oman) and the northeastern lepida group (from Turkey through India). However, the characters presented to justify this grouping are variable and show a mosaic pattern, and whether genetic and vocal differences exist is unknown. We found consistent between-group song differences, with the nominate group giving consistently longer inter-phrase intervals, whereas the members of the lepida group sing an essentially continuous reel. An mtDNA tree suggests a deep split between the nominate and lepida groups, with a coalescence time between these clades of ~ 2.2 million years ago. Vocal and mtDNA analyses provided evidence that the northeastern Arabian Peninsula taxon carpenteri belongs to the lepida group. We found that, of all the morphological characters proposed, only proportions and tail barring and spotting relatively consistently distinguish the 2 groups. However, these characters strongly suggest that the eastern Arabian Peninsula is populated by taxa of both the gracilis and lepida groups, in different areas, but we lack genetic and bioacoustic data to corroborate this. Although further study is needed in potential contact zones, we suggest that 2 species should be recognized in the P. gracilis complex, and we propose the retention of the English name Graceful Prinia for P. gracilis sensu stricto, while we suggest that P. lepida be known as Delicate Prinia.

opencc-zeroMar 2022View details →