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Fig. 1 in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)

Fig. 1 Distributional limits of Sericornis and Crateroscelis in the Australo-Papuan region. Distribution of the Australo-Papuan-centred group is shown in the main figure. The white-browed scrubwren (S. frontalis) complex has the broadest distribution in Australia (stippled area) and is divided into an eastern frontalis and western maculatus group. The remaining Australian scrubwrens are restricted to the east

Fig. 6 in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)

Fig. 6 Biogeographic reconstruction showing possible routes of dispersal as a function of asynchronous Central Range orogeny and eustatic falls in sea level. a Initial colonisation of western New Guinea during the late Miocene after the onset of orogeny in western new Guinea ~ 12 Mya. Colonisation from northern Australian mesic forests is inferred to have occurred during periods of lowered sea level when a deltaic environment, formed by the accumulation of shedding siliclastics, developed on the Arafura shelf. b Pliocene diversification of New Guinean sericornithinines coincides with a phase or rapid mountain uplift and suggests passive transport of species to higher elevations. c Pleistocene connectivity across the Torres Strait in the magnirostra group coincident with periods of lower sea level during glacial maxima. Dispersal across the Arafura shelf is unlikely at this time due to the contraction of mesic

Fig. 4 in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)

Fig. 4 Maximum clade credibility tree for the Sericornithinae generated in BEAST using a strict molecular clock and Yule speciation prior. Species names for scrubwrens and mouse-warblers are in black type with altitudinal replacement sequences in shaded boxes. Alternative placement of S. citreogularis supported by Bayesian hypothesis testing is indicated by the dashed arrow linking branches. Mean node ages (Mya) are shown

Fig. 5 3D in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)

Fig. 5 3D plot of principal components of ecomorphological divergence in New Guinean Sericornis and Crateroscelis. Letters A–D denote the four altitudinal replacement sequences recovered in the phylogenetic tree (Fig. 4). The figure was prepared in scatterplot3D and Adobe Illustrator CS6 (colour available online)

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Data from: Evolution of codfishes (Teleostei: Gadinae) in geographical and ecological space: evidence that physiological limits drove diversification of subarctic fishes

Aim: To develop a holistic biogeographical history of codfishes in the subfamily Gadinae based on historical relationships, ecological niche, and evolution of physiological tolerances. Two alternative diversification scenarios were tested in two co-distributed, Northern Hemisphere clades: (1) clade ancestors were temperate, and environmental niche has been conserved over evolutionary time, implying that speciation was driven by vicariance associated with ice sheet formation; and (2) clade ancestors were Arctic, and species convergently adapted to temperate environmental conditions, implying that speciation was driven by repeated adaption to temperate environments. Location: Northern Hemisphere Arctic and subarctic oceans. Methods: Fifty-five new sequences of four genes from 23 tissue samples were combined with 10 GenBank sequences to generate a time-calibrated phylogenetic hypothesis. Combining the phylogeny with information on species' ecological niche tolerances inferred from correlational models, I reconstructed ancestral environmental tolerances of each of the focal clades. These results were combined with Bayesian area-based biogeographical analysis and regional palaeoclimatic history to develop a holistic biogeographical history of Gadinae. Results: Of 18 environmental variables describing species' tolerances to salinity, temperature, sea ice concentration, and mixed layer depth, only mean, maximum and minimum sea bottom temperature, and mean and minimum sea surface temperature showed phylogenetic signal across Gadinae. Both ecological niche and geographical distributions of gadine fishes are largely conservative, but two clades contain both Pacific and Atlantic species. Focal clade divergence time estimates suggest a Pliocene origin for both, with further Pleistocene divergence. Main conclusions: Reconstructed ancestral environmental tolerances of crown cods and tomcods support a temperate origin of both groups. The timing of diversification of these two clades and the intolerance of temperate species to sea ice suggest that cyclical Arctic ice formation drove divergence. Future sea ice reduction may have dramatic consequences for distributions and persistence of commercially important species when currently allopatric temperate species come into secondary contact.

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Data from: Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies

Rapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. Neotropical Adelpha butterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history of Adelpha and its temperate sister genus Limenitis using genomewide restriction-site-associated DNA (RAD) sequencing. Despite a declining fraction of shared markers with increasing evolutionary distance, the RAD-Seq data consistently generated well-supported trees using a variety of phylogenetic methods. These well-resolved phylogenies allow the identification of an ecologically important relationship with a toxic host plant family, as well as the confirmation of widespread, convergent wing pattern mimicry throughout the genus. Taken together, our results support the hypothesis that evolutionary innovations in both larvae and adults have permitted the colonization of novel host plants and fuelled adaptive diversification within this large butterfly radiation.

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Figure 12 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 12. Response curve of the maximum entropy (Maxent) model. A, response curves of the precipitation of the coldest quarter, used to calculate the western operational taxonomic unit (OTU) Maxent model of the Eirenis persicus species group; B, response curves of the minimum temperature of the coldest month (°C), used to calculate the nigrofasciatus and eastern OTU Maxent model of the E. persicus species group. The logistic prediction values changed as each environmental variable was varied one by one whilst keeping all other environmental variables at their average sample value. In (A), boxplots represent the precipitation of the coldest quarter in the habitat of E. persicus specimens in southwestern Iran (SW-IR), Turkey and western Iran (TK, W-IR), and northern Iran (N-IR); in (B), boxplots represent the minimum temperature of the coldest month (°C) in the habitat of E. persicus specimens of the nigrofasciatus OTU (nig), eastern Iran and Turkmenistan sub-OTU (E-IR, TM), north-eastern Pakistan sub-OTU (NE-PK), and specimens referred to Eirenis mcmahoni (mc).

Figure 11. Predicted suitable habitat for the Eirenis persicus species group. A in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 11. Predicted suitable habitat for the Eirenis persicus species group. A, western operational taxonomic unit (OTU) specimens; B, eastern and nigrofasciatus OTUs. The model was reclassified into ten equal probability classes. Only classes with probabilities greater than 60% are presented here. Maximum training sensitivity plus specificity logistic threshold (dark grey) is equal to 15.7% in (A) and 23% in (B). In (A), circles indicate the south-western Iran sub-OTU, ◆ indicate the south-eastern Turkey and western Iran sub-OTU, and plus symbols indicate the northern Iran specimens. In (B), circles indicate specimens of the nigrofasciatus OTU, triangles indicate the eastern Iran and Turkmenistan sub-OTU, plus symbols indicate the north-eastern Pakistan sub-OTU, and stars indicate the localities of the specimens referred to Eirenis mcmahoni.

Figure 10 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 10. Median joining network of Eirenis persicus cytochrome b haplotypes. Abbreviations: PE, E. persicus specimens with persicus morph with bases of their anterior dorsal scales are darker, PW, persicus morph with unicoloured dorsal scales; W, walteri morph; nigrofasciatus, nigrofasciatus morph. Numbers indicate the number of nucleotide substitutions.

Figure 9 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 9. Maximum likelihood chronogram representing the evolution of the genus Eirenis and its immediate ancestors, as well as the hypothetical ancestral distribution of Eirenis persicus over the Eurasia plate. A, divergence of E. persicus (vertical line) from the Eirenis lineage (square) 16–18 Mya. B, divergence of E. persicus into the western and eastern clades 10–13 Mya. Abbreviations: Pleis., Pleistocene; Plioc., Pliocene.

Figure 8 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 8. Bayesian inference tree of the members of the Eirenis persicus species group and their relatives. Branch support measures are Bayesian posterior probabilities (×100)/maximum likelihood bootstrap support (the latter value presented only for the E. persicus species group). Abbreviations: PE, E. persicus specimens of the persicus morph with bases of their anterior dorsal scales are darker than the rest of scales; PW, persicus morph with unicoloured dorsal scales; W, walteri morph; nigrofasciatus, nigrofasciatus morph. The scale bar shows the length of branch that represents 3% genetic divergence.

Figure 3 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 3. Geographical positions of the different operational taxonomic units (OTUs): eastern OTU (dotted line), western OTU (dashed line), nigrofasciatus OTU (solid line), novum OTU (stars).

Figure 2 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 2. All available distribution records of the Eirenis persicus species group. Circles indicate the E. persicus specimens, with the persicus morph bearing unicoloured dorsal scales; squires indicate specimens from eastern Iran, southern Turkmenistan, and southern and western Pakistan, having both persicus morph that base of their anterior dorsal scales are darker, and walteri morph; stars indicate specimens referred to Eirenis mcmahoni (Wall, 1911); plus symbols indicate specimens in north-eastern Pakistan, having both persicus morphs that base of their anterior dorsal scales are darker, and with walteri morph; asterisks indicate specimens with the novum pattern; triangles indicate specimens of the nigrofasciatus morph. Circle 29 indicates the type locality of Cyclophis persicus Anderson, 1872; squire 2 indicates the type locality of Pseudocyclophis walteri Boettger, 1888; squire 7 indicates the type locality of Contia zebrina Wall, 1923; triangle 6 indicates the type locality of Contia persica var. nigrofasciata Nikolsky, 1907; star 3 indicates the type locality of Contia angusticeps Boulenger, 1894; plus symbols 2–5 indicate the type series localities of Contia mcmahoni Wall, 1911. For more details, see Appendix 1.

Figure 1 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 1. Different morphs of the Eirenis persicus species group: A, persicus morph from Dasht-e Arjan, Fars province, south-western Iran (photo by F. Hidary); B, walteri morph from Dehbakri, Kerman province, south-eastern Iran (photo by R. Nazarov); C, new morph from Sisakht, Yasuj province, central Zagros mountains, Iran (photo by H. Esmaeili); D, persicus morph from Kafir Kot, Khyber Pakhtunkhwa Province, Pakistan (photo by R. Masroor); E, nigrofasciatus morph from Dezful, Khuzestan province, south-western Iran (photo by F. Hidary).

Figure 14 in Alpine-Himalayan orogeny drove correlated morphological, molecular, and ecological diversification in the Persian dwarf snake (Squamata: Serpentes: Eirenis persicus)

Figure 14. Dorsal body (A), dorsal head (B), and lateral head (C) view of the holotype of Eirenis (Pseudocyclophis) occidentalis sp. nov.