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Figure 3. Consensus tree for the cytochrome b in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago

Figure 3. Consensus tree for the cytochrome b dataset for representative genotyped specimens of the Rhinolophus hildebrandtii complex. The topology represents the consensus topology from a 20 million MCMC run implemented in BEAST. Estimates of divergence times (million years ago; Mya) are indicated adjacent to nodes or above branches and grey bars indicate 95% HPD values. The split between the Hipposideridae and Rhinolophidae was used as the calibration point. Taxa names include museum/field numbers which correspond to Appendix S1 or GenBank accession numbers and abbreviations are: RcfH - R. cf. hildebrandtiiı RD - R. darlingiı RE - R. eloquensı RF - R. fumigatusı RH - R. hildebrandtii s.l.ı RL - R. landeri and RR - R. ruwenzorii. Localitiesı where availableı are providedı abbreviations include SA - South Africaı MZ - Mozambiqueı and ZW - Zimbabweı and the numbers in parentheses correspond with place names in Table S1 and Fig. 2 for Clade 1 and 2 individuals. doi:10.1371/journal.pone.0041744.g003

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Figure 7 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago

Figure 7. Relative warps analysis (RWA) of 12 lateral cranial landmarks from 23 individuals of R. hildebrandtii s.l. belonging to two molecular clades and two lineages of Clade 1 (see Fig. 3). Revised taxon names are provided in parentheses (see Taxonomic Conclusions). Skulls which were included in this analysis are indicated in Table S1. Symbols as is in Fig. 5. Thin plate splines (grids) show landmark distortions represented by extremes of variation on RW1 (left = negative; right = positive) and RW2 (bottom = negative; top = positive) axes. The two skull photographs at the bottom are of actual specimens representing the negative (left: DM 8577ı mossambicus from Namapaı Mozambique) and positive (right: DM 11560ı cohenae from Mayoı Mpumalanga Province) extremes of variation on RW1. Landmark positions (filled circles) are shown in the photograph in the centre. doi:10.1371/journal.pone.0041744.g007

Figs 41–50 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 41–50. Discostella gabinii Paillès & Sylvestre sp. nov., Lake Petén-Itzá (Guatemala); LM valve views. 41–42. Modern specimens of D. gabinii sp. nov. from Cenote Juarez. 43–44. Modern specimens of D. gabinii sp. nov. from Lake Amatitlan. 45–50. Type material of fossil lacustrine diatom D. gabinii sp. nov. 45. Holotype (MNHN, slide PC060873). 48–50. A shadow line is visible in large specimens. Scale bar = 10 µm.

Figs 25–32 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 25–32. Type material of fossil lacustrine diatom Cyclocostis rolfii Paillès gen. et sp. nov.; SEM external valve views. 25. Valve view of concentrically undulated marginal area and tangentially undulated central area; punctuated striae become in the central area rows of larger areolae arranged in a stellate pattern. 26. Valve surface with scattered papillae; the external opening of the single valve face fultoportula is located on the raised part (white arrowhead). 27. Marginal area showing the external openings of marginal fultoportulae, collared but with no projections (white arrowheads). 28. Side view of marginal area showing striation, papillae, external openings of marginal fultoportulae (mfp – two white arrows), and the cingulum consisting of an open valvocopula and several copulae (white arrow). 29. Detail of the central area with large areolae; external areolae are bigger and occluded by volae in places where ribs are fusing. 30. Broken valve view showing the different striation between the margins and the center, the steep transversal undulation and the valve thickness. 31. Marginal area with the external openings of marginal fultoportulae (white arrowheads), papillae, and the cingulum. 32. Broken valve view showing the simple structure of anastomosing ribs covered by a finely perforated silica layer. Scale bars: 25 = 5 µm; 26, 28–32 =2 µm; 27 = 1 µm (27).

Fig. 59 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Fig. 59. Diagram showing the succession of Stephanodiscaceae Glezer & Makarova in Pleistocene sediments (0–84 ka) from Lake Petén-Itzá (Guatemala).

Figs 1–24 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 1–24. Type material of fossil lacustrine diatom Cyclocostis rolfii Paillès gen. et sp. nov., Lake PeténItzá (Guatemala); LM girdle view (1) and valve views (2–24). 4. Holotype (MNHN, slide PC0608731). 7–8. Valve surface strongly tangentially undulated, forming an S shape. Scale bar = 10 µm.

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IODP Expedition 382: Supplementary Tables for "New magnetostratigraphic insights from Iceberg Alley on the rhythms of Antarctic climate during the Plio-Pleistocene"

Supplementary tables for "New magnetostratigraphic insights from Iceberg Alley on the rhythms of Antarctic climate during the Plio-Pleistocene" Includes stratigraphic data for International Ocean Discovery Program (IODP) Expedition 382 Sites U1536 and U1537.   Table Captions: Table S1. Splice table and additional appended cores for Site U1536 used in this study.   Table S2. Splice table and additional appended cores for Site U1537 used in this study.   Table S3. Correlation table for creation of correlated equivalent depth (ced) scale between Sites U1536 and U1537. Table S4. Uncertainty estimates for Site U1536 natural gamma radiation (NGR) correlation to Site U1537 on mcd depth scale using Undatable (Lougheed & Obrochta, 2019).   Table S5. Site U1536 inclination, natural gamma radiation (NGR), gamma ray attenuation (GRA), and b* data used in this study. Table S6. Site U1537 inclination, natural gamma radiation (NGR), gamma ray attenuation (GRA), and b* data used in this study. Table S7. Meters below sea floor (mbsf) depths of magnetic reversals at Site U1536. Reversal ages are those used in this study’s age models (see Methods; Channell et al., 2016; Lisiecki & Raymo, 2005). Table S8. Meters composite depth (mcd) splice depths of magnetic reversals at Site U1536.  Reversal ages are those used in this study’s age models (see Methods; Channell et al., 2016; Lisiecki & Raymo, 2005). Table S9. Meters below sea floor (mbsf) depths of magnetic reversals at Site U1537. Reversal ages are those used in this study’s age models (see Methods; Channell et al., 2016; Lisiecki & Raymo, 2005). Table S10. Meters composite depth (mcd) splice depths of magnetic reversals at Site U1537.  Reversal ages are those used in this study’s age models (see Methods; Channell et al., 2016; Lisiecki & Raymo, 2005). Table S11. Magnetostratigraphic age model for Site U1536 generated with Undatable (Lougheed & Obrochta, 2019). Table S12. Magnetostratigraphic age model for Site U1537 generated with Undatable (Lougheed & Obrochta, 2019). Table S13. Dove Bain data stacks used in this study.   Table S14. Stratigraphic summary of magnetic reversals discussed in this study.  U1308 ages from Channell et al., 2016.  In relation to benthic δ18O, warm intervals are intervals with more positive values.  In relation to Dove Basin facies, warm intervals are intervals with high higher b*, lower NGR, and lower GRA.

Fig. 2 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species

Fig. 2. Phylogenetic tree of the Bayesian Inference of the Bagre derived from the concatenated database of the Cytb 1 and ATPase 8/6 genes. Only unique haplotype are included here. The first value on each branch corresponds to the ML support value and the second one to the BI. Only support values and posterior probabilities above 60% are shown. Grey = northern Brazilian coast lineage, including the semi-arid sector of the northeast coast; Black = southern Brazilian coast.

Fig. 6 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species

Fig. 6. Scatterplots of the principal components PC1 and PC2, obtained from the analysis of one meristic and nine morphometric variables in Bagre bagre, with factor loadings for the first principal components. Abbreviations: E, east Brazilian coast; h, humid northeastern coast of Brazil; N, northern Brazilian coast; sa, semi-arid northeastern coast of Brazil; S, southeast Brazilian coast.

Fig. 4 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species

Fig. 4. Genealogiesofthehaplotypesof (A) themitochondrial Cytb gene, based on the TIM2+I+G evolutionary model, and (B) the mitochondrial ATPase 8/6 gene, based on the HKY+G model. Green = northern Brazilian coast influenced by the Amazon–Orinoco plume, Light blue = semi-arid northeastern coast, Orange = southeastern coast.

Fig. 1 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species

Fig. 1. Geographic distribution of the two Bagre bagre lineages found in South America [red triangle = northern Brazilian coast, including region dominated by the plume of the Amazon and Orinoco rivers and semi-arid sector of Brazilian northeast coast (light blue = mouth of the Orinoco River; black circle = Macapá, AP; dark blue circle = Bragança, PA; yellow = São Luis, MA; green = Fortaleza, CE), and inverted black triangle = eastern and southern Brazilian coast, including the humid sector of the northeast coast (white circle = Santos, SP)] showing the number of specimens analyzed in each region (not bold = morphological analysis, and bold = molecular analysis). Green = northern Brazilian coast influenced by the Amazon– Orinoco plume, Light blue = semi-arid northeastern coast of Brazil; Dark blue = humid northeastern coast of Brazil, Yellow = east coast, and Orange = southeast coast).

Fig. 3 in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species

Fig. 3. Bayesian strict clock chronogram based on the 1535 bps of the concatenated genes (Cytb and ATPase 8/6). The calibration points and evolutionary rates were based on Betancur-R. & Armbruster (2009).

Fig. 7. A in Early Pleistocene lineages of Bagre bagre (Linnaeus, 1766) (Siluriformes: Ariidae), from the Atlantic coast of South America, with insights into the demography and biogeography of the species

Fig. 7. A. Occurrence of Bagre bagre, Bagre marinus and other species of the genera Amphiarius, Aspistor, Cathorops, Genidens, Notarius, and Sciades, on the Atlantic coast of South America. Numbers of the lots deposited in zoological collections.

Fig. 3 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 3. Sedimentary log, paleontological sampling points, microfauna assemblages and paleosalinity estimation in the Goychay section.

Fig. 8 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 8. Sedimentary log, paleontological sampling points, microfauna assemblages and paleosalinity estimation in the Hajigabul section.

Fig. 7 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 7. Magnetostratigraphy of the Goychay section. In columns, from left to right: Regional (local) stages; Depositional units; Lithological log; Biostratigraphic sampling points: green - mollusc samples, blue - microfauna samples; Magnetic susceptibility (plotted on a logarithmic scale; black line - values for each sample, red line - averaged 3); Inclination; Declination; Interpreted polarity (black - normal, white - reversed). The Akchagylian - Apsheronian transition is drawn based on microfauna (lower limit) and macrofauna (upper limit). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 12 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 12. Magnetostratigraphy of the Hajigabul section. In columns from left to right: Regional stages; Depositional units; Lithological log; Biostratigraphic sampling points, where green points are mollusc samples and blue points - microfauna samples; Magnetic susceptibility (plotted on a logarithmic scale)); Inclination; Declination; Interpreted polarity. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 2. Lithostratigraphic subdivision of the Goychay section (A) and the Hajigabul section (B). Logs, general view and characteristic photos of each sedimentary unit.

Fig. 1 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 1. Location map of the Goychay and Hajigabul sections. Columns on the left: Global polarity time scale (Hilgen et al., 2012) Epoch/Age; Regional Stages: a* classical definition (Shantser, 1982; Arslanov et al., 1988; Nevesskaya et al., 2003, 2004), b* this study. Position of the studied sections in relation to the Caspian Sea (A) and to the Kura Basin (B) (The map base is taken from www.maps-for-free.com); Geological maps for the Goychay section (C) and the Hajigabul section (D) modified after Bairamov et al. (2008).

Fig. 13 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 13. Correlation of polarity patterns to the Global Polarity Time Scale (GPTS), the main paleoenvironmental events and characteristic mollusc fauna in the Goychay and Hajigabul sections. Sedimentation rate curves: Hajigabul section (A), the Goychay section (B).