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Figure S1 in New Insights into the Taxonomy of Myotis Bats in China Based on Morphology and Multilocus Phylogeny

Figure S1. Phylogenetic trees reconstructed based on 123 mitochondrial Cytb haplotypes. Values on the branches represent posterior probability obtained with MrBayes (A) and bootstrap percentage obtained with IQ-TREE (B). Geometries of different colors and shapes represent Myotis species. The information on mitochondrial haplotypes was described in Table S3.

Figure 2 in New Insights into the Taxonomy of Myotis Bats in China Based on Morphology and Multilocus Phylogeny

Figure 2. Principal component analysis based on five morphological characteristics. The first two principal components explained 88.77% and 6.77% of the total variance, respectively. Geometries with different colors and shapes represent Myotis species.

Figure 4 in New Insights into the Taxonomy of Myotis Bats in China Based on Morphology and Multilocus Phylogeny

Figure 4. (A) Species tree constructed in *BEAST based on Cytb, Rag2, and Chd1 genes. Values on the branch represent posterior probability. (B) Heatmap of K2P genetic distance calculated based on mitochondrial Cytb gene (lower triangular) and concatenated nuclear genes (upper triangular). Geometries with different colors and shapes represent Myotis species and corresponds to the species on the left side.

Figure 1 in New Insights into the Taxonomy of Myotis Bats in China Based on Morphology and Multilocus Phylogeny

Figure 1. Mitochondrial phylogenetic tree reconstructed based on 123 Cytb haplotypes. Values on the branches represent posterior probability (PP) and bootstrap percentage (BP). Geometries with different colors and shapes represent Myotis species. "Initial" represents the initially filed identification or the species information labelled in GenBank. "Revised" means the revised species names. The information on mitochondrial haplotypes was described in Table S3.

Figure S2 in New Insights into the Taxonomy of Myotis Bats in China Based on Morphology and Multilocus Phylogeny

Figure S2. Phylogenetic trees reconstructed based on 20 nuclear Rag2 haplotypes (A‒B), 13 nuclear Chd1 haplotypes (C‒D), and concatenated nuclear sequences (E‒F). Values on the branches represent posterior probability obtained with MrBayes (BI) and bootstrap percentage obtained with IQ-TREE (ML). Geometries of different colors and shapes represent Myotis species. The information on nuclear haplotypes was described in Table S4.

Figure 3 in New Insights into the Taxonomy of Myotis Bats in China Based on Morphology and Multilocus Phylogeny

Figure 3. (A) Phylogenetic tree based on concatenated nuclear genes. Values on the branches represent posterior probability (PP) and bootstrap percentage (BP). (B) Species tree constructed in *BEAST based on nuclear Rag2 and Chd1 genes. Values on the branch represent posterior probability. Geometries with different colors and shapes represent Myotis species.

publicJan 2025View details →

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UnFATE: A comprehensive probe set and bioinformatics pipeline for phylogeny reconstruction and multilocus barcoding of filamentous ascomycetes (Ascomycota, Pezizomycotina)

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opencc-zeroDec 2018View details →

Data from: A multilocus phylogeny of the fish genus Poeciliopsis: solving taxonomic uncertainties and preliminary evidence of reticulation

The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, i.e., concatenated (also known as super-matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously considered of undetermined taxonomic status could be unequivocally assigned to P. scarlli; revealing a relatively recent dispersal event across the Trans Mexican Volcanic Belt (TMVB) or Pacific Ocean, which constitute a strong barrier to north-south dispersal of many terrestrial and freshwater taxa. The closest relatives of P. balsas, a species distributed south of the TMVB, are distributed in the north; representing an additional north–south split in the genus. An undescribed species of Poeciliopsis, with a highly restricted distribution (i.e., a short stretch of the Rio Concepcion; just south of the US-Mexico border), falls within the Leptorhaphis species complex. Our results are inconsistent with the hypothesis that this species originated by "breakdown" of an asexual-hybrid lineage. On the other hand, network analyses suggest one or more possible cases of reticulation within the genus that require further evaluation with genome-wide marker representation and additional analytical tools. The most strongly supported case of reticulation occurred within the subgenus Aulophallus (restricted to Central America), and implies a hybrid origin for P. retropinna (i.e., between P. paucimaculata and P. elongata). We consider that P. balsas and P. new species are of conservation concern.

opencc-zeroDec 2015View details →

Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot

We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of geographic structure in a unique archipelago-endemic radiation. Philippine Gonocephalus have previously escaped the attention of biogeographers, due to taxonomic confusion associated with low numbers of preserved specimens in museum collections. With new vouchered material and genetic sampling from a comprehensive, archipelago-wide vertebrate biodiversity inventory, our findings join many recent studies highlighting the unprecedented faunal diversity in one of the world's most unique biodiversity conservation hotspots.

publicAug 2016View details →

Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot

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publicJan 2019View details →

Data from: A multilocus phylogeny of the fish genus Poeciliopsis: solving taxonomic uncertainties and preliminary evidence of reticulation

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FIGURE 10 in Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas

FIGURE 10. Distribution of Acanthodactylus montanus (squares) and Acanthodactylus lacrymae (diamonds) based on specimens examined in this study. Coloured dots represent specimens of the three main phenotypes (none is monophyletic in the mtDNA or nDNA trees) in Morocco based on Bons and Geniez 1995. Specimens with the "bellii" phenotype in the High Atlas are almost certainly montanus and lacrymae. White symbols represent specimens tentatively identified as A. montanus (square) or A. lacrymae (diamond, see text). The continuous white lines represent the currently known distribution of the new species while dotted white lines represent possible extensions of the distribution if tentative identifications are correct. The dotted dark blue line represents the southernmost extension of confirmed IM clade specimens based on our field sampling.

FIGURE 8 in Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas

FIGURE 8. Holotypes of Acanthodactylus montanus sp. nov. (MNHN-RA-2018.0026, Tizi n'Tichka) and (B) Acanthodactylus lacrymae sp. nov. (MNHN-RA-2018.0027, Tislit) with a picture of the habitat of this species (Isli lake). Photo credits: A (PAC), B (PG).

FIGURE 5 in Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas

FIGURE 5. Haplotype networks (nDNA) showing the amount of allele sharing between the two mountain clades (EHA in A and WHA in B) and their respective neighbouring populations from the IM clade. The blue asterisks highlight haplotypes of the sample from Ouaourioud (IM clade), located only 10 km from the Tislit population (EHA clade).

FIGURE 2 in Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas

FIGURE 2. Comparison of phylogenetic trees inferred for the Acanthodactylus erythrurus species complex from (A) the mtDNA data-set and (B) the concatenated nuclear data-set. Tree topologies have been inferred by the Maximum Likelihood approach (bootstrap proportions are presented in percentage, and are followed by the posterior probabilities obtained from the Bayesian analyses, topology not shown). Additionally, clusters inferred by barcode gap approach (ABGD) have been represented by white vertical bars reported on the mtDNA tree (A). Localities abbreviations are detailed in Table S5.

FIGURE 1 in Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas

FIGURE 1. Distribution of the Acanthodactylus erythrurus complex (based on www.iucnredlist.org, green shading) and location of the samples used in this study for genetic analyses. Symbols represent the five main lineages identified in this study (light blue dots = IM, red squares = WHA, pink diamonds = EHA, dark purple downward triangles = CA, lavender upward triangles = AT, cf. Figs 2, 3).

Appendix I in Morphology and multilocus phylogeny of the Spiny-footed Lizard (Acanthodactylus erythrurus) complex reveal two new mountain species from the Moroccan Atlas

Appendix I. Comparison of the most relevant morphological characters for each of the main clades. For quantitative traits, ranges are given followed by the mean ± the standard deviation, with sample size in parentheses. Qualitative traits are expressed in percentage. (2A) quantitative morphometric variables. (2B) quantitative (pholidosis and colouration) and qualitative (colour pattern or scales shape) variables. For some bilateral characters, the sample size was noted as the number of sides rather than specimens. M: males, F: females, J: juveniles and subadults.

FIG. 4 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

FIG. 4. Monophyly of North American Gryllus is strongly supported by (A) RAxML analysis of concatenated data (492,531 bp) with bootstrap values, and by (B) Astral analysis of gene trees (563 loci) with quadripartition branch support values.

FIG. 7 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

FIG. 7. Phylogeny of Gryllus panel 1 of 4. RAxML tree (left) with taxon names; Astral tree (right) with thin lines connecting tips to taxon names. Support value color codes:> 90% = bright green;> 80% and <90% = green;> 70% and <80% = olive;> 60% and <70% = orange/brown;> 50% and <60% = red; <50% = black

FIG. 2 in Multilocus phylogeny of Gryllus field crickets (Orthoptera: Gryllidae: Gryllinae) utilizing anchored hybrid enrichment

FIG. 2. Alexander's first phylogeny of US Gryllus principally based on life-cycle considerations. Redrawn from Alexander (1968). * Note: G. texensis was labeled as G. integer in Alexander's original figure, see Cade & Otte (2000).