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Fig. 3. A 50 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 3. A 50% majority rule consensus tree from MSC-bootstrap analysis of the "All individuals" dataset. Color labels as in figures 1 and 2.

Fig. 2 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 2. Maximum likelihood tree of the "All individuals" concatenated dataset generated with IQ-TREE.Topology with branch lengths in substitutions/site shown in bottom left. Black dots indicate deeper nodes with bootstrap and SH-like aLRT both under 90, otherwise deeper nodes are above 90. Support values for shallow nodes not shown.

Fig. 1 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 1. Collection locations in western North America. Colors for S. MCCooki are based on phylogenetic group assignment (see Fig. 2). Female (left) and male (right) S. MaxiMa from Davis, CA shown in inset.

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Fig. 3 in Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes

Fig. 3. Multi-species coalescent (MSC) phylogenies of the Australasian/Indomalayan clade including the bourbonica complex, generated in ASTRAL-III using 75% complete alignment matrices. (A) (left) represents the unphased MSC analysis and (B) (right) represents the phased MSC analysis.Values on the internal nodes represent local posterior probabilities (LPP), with ≥0.95 indicating strong support and ≤0.75 indicating weak support. Scale bars under phylogenetic trees indicate the number of substitutions per site. Photos of N. bourbonica (Ny201) and N. vaga (Ny204) workers in profile view are to scale and were taken by Milan Janda.

Fig. 5 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 5. Cluster analysis of unlinked SNPs using VAE and carapace length of (a) male and (b) female individuals from Davis, CA. Individuals with carapace length (a)>8.5 mm (male) and (b)>10.0 mm (female) are indicated as S. MaxiMa.

Fig. 4 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 4. Cluster analysis of unlinked SNPs using VAE for "Western group" individuals. Individuals are assigned to clades from the concatenated analysis (see Fig. 1).

Fig. 8 in Phylogenomic Variation at the Population-Species Interface and Assessment of Gigantism in a Model Wolf Spider Genus (Lycosidae, Schizocosa)

Fig. 8. Waveforms from substrate-borne vibrations produced by males in response to female pheromone cues. Phylogeny is based on maximum likelihood analysis of the concatenated dataset generated with IQ-TREE (see Fig. 2).

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Fig. 6 in Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes

Fig. 6. Species delimitation hypotheses of the fulva + guatemalensis complexes. (Left) Cloudogram based on the STACEY analysis using 609 SNPs extracted from the 'fg37-phased_90p' dataset, with the 'root canal' (blue) summarizing the main features of the tree set. (Right) Summary of species delimitation schemes based on morphospecies sorting and for each analysis performed in this study, with each different colored bar (also labeled with different letters) representing a single species.

Fig. 4 in Pitfalls in supermatrix phylogenomics

Fig. 4. Distribution of missing data in phylogenomic datasets. The raw dimensions of a supermatrix (in numbers of genes and taxa) should always be accompanied by an estimate of its level (and ideally distribution) of missing data (A). Indeed, some datasets were advertised as very large when published but required a lot of useless computing power due to a large proportion of missing data (B). More importantly, such datasets are more exposed to data errors, systematic error and phylogenetic artefacts, as their effective number of species is actually quite low for the largest part of their width. In other cases, a targeted completion (in the outgroups) was enough to improve the phylogenetic accuracy (D–E). In contrast, datasets assembled with the optimal phylogenomic zone in mind combine a suffcient number of genes and taxa while featuring a low proportion of missing data (C). These are the most appropriate datasets to produce accurate phylogenetic relationships.

Fig. 2 in Pitfalls in supermatrix phylogenomics

Fig. 2. Example of a frameshift-aware alignment produced by MACSE. Trpc2(-like) sequences of bats were aligned at the nucleotide level (A) and amino acid level (B), unravelling several frameshifts (indicated by "!") and stop codons (indicated by "*") in the pseudogenes. Hence, MACSE automatically provided an alignment that would otherwise require a lot of tedious manual work. It can also be used to replace these frameshifts and stop codons by standard codons (e.g., "NNN" or "---") in order to obtain an alignment suitable for further analysis with standard tools (e.g., PhyloBayes or PAML).

Fig. 1 in Pitfalls in supermatrix phylogenomics

Fig. 1. Evolution of phylogenetic reconstruction over time. Different zones can be delimited based on the number of genes (X axis) and number of taxa (Y axis) composing the supermatrix at hand. Generally speaking, the (upper) left part of the map has more to do with identifying species (as in barcoding studies), while the right part of the map corresponds to multigene and phylogenomic datasets assembled for recovering large-scale phylogenetic relationships. Each of these zones suffers from its own combination of issues (stochastic error, systematic error, data errors, computational requirements and missing data). Interestingly, the "optimal zone" in phylogenomics is not the one corresponding to the highest number of genes and taxa, because this computationally "intractable zone" is also the one where data errors and missing data are the most abundant. The latter aspect is due to the continuous shrinking of the number of orthologous genes when considering increasingly more species, owing to gene loss, gene duplication and gene transfer events.

Fig. 3 in Pitfalls in supermatrix phylogenomics

Fig. 3. Typical output of Phylo-MCOA. A matrix containing as many rows as the number of species and as many columns as the number of genes was computed, in which complete (black arrows) and cell-bycell (dashed circles) outliers can easily be detected. Cells with a high value (dark grey) represent species whose position in a given gene is not concordant with their position in all the other genes. It is thus a measure of distance to the common signal present in the data.

FIGURE 6 in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

FIGURE 6. Ventral view of folded phallic lobes, in adult male Ammopelmatus sp., from Santa Clara County, California. Same species as illustrated in Fig. 4. (L) lateral lobe; (V) ventral lobe. Photo Chris Grinter.

FIGURE 3 in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

FIGURE 3. Male (top) Ammopelmatus sp. with yellowish colored phallic lobes (arrow) fully unfolded and almost making contact with female below him. Photo DBW.

FIGURE 2 in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

FIGURE 2. Third, but unnamed, species of Stenopelmatus from Costa Rica, this specimen from Ascensión Chirripó, Cartago Province, 9.463525° -83.571862°. Photo Jorge Gutiérrez-Rodríguez.

FIGURE 5 in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

FIGURE 5. Ventral view of folded phallic lobes, in adult males, all from type localities. (A) S. zimapan (DBW Stop 11-66); (B) S. piceiventris (DBW Stop 06-36); (C) S. typhlops (DBW Stop 08-44); (D) Dorsal view, same specimen as in Fig. 5C. (L) lateral lobe; (V) ventral lobe. Photos Chris Grinter.

FIGURE 4 in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

FIGURE 4. Inflated and unfolded phallic lobes, as prepared in live Ammopelmatus sp., from Santa Clara County, California: a. Posterior view. b. Lateral view. (C) cerci; (H) black hooks, confirming adult status; (L) lateral lobes; (S) subgenital plate; (V) ventral lobes. Photos Chris Grinter.

FIGURE 1 in Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

FIGURE 1. Orthoptera-specific target enrichment (OR-TE) analysis. We find both families Anostostomatidae and Stenopelmatidae (as indicated by an *) to be paraphyletic. Family Schizodactylidae is shown to be distantly related to both Anostostomatidae and Stenopelmatidae.