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Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories
<p>The following files are contained in this repository:</p> <p><br> README.Hume_et_al_2022.zenodov4.txt - This document.</p> <p>scripts.Hume_et_al_2022.zenodov4.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript.</p> <p>acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study.</p> <p>TaraPacific_SST_timeseries_mean_productsV2mai2021.Hume_et_al_2022.zenodov1.csv - The historical temperature data set used for the RDA, Mantel tests and gradient Forest analysis.</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as 'raw' in the Methods of the associated manuscript.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs.</p> <p>Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as 'target genes' in the Methods of the associated manuscript.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome.</p> <p> </p> <p>mtORF Phylogeny</p> <p>TP-Johnston_mtORF-Pocillo.fa = all sequences</p> <p>TP-Johnston_mtORF-Pocillo.mafft.fa = mafft alignment</p> <p>TP-Johnston_mtORF-Pocillo.mafft.ML.nwk = ML tree newick</p> <p> </p> <p>Hellberg genotype network Porites</p> <p>TP-Hellberg_MM32-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_MM100-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_ATPaseB.nex = all aligned sequences for this locus with indels encoded,</p> <p>TP-Hellberg_POFAD.nex = POFAD multilocus genotypic distance,</p> <p>TP-Hellberg_Splitstree.nex= Multilocus genotype network in nexus format</p> <p><br> Gradient Forest Analysis</p> <p>Poc_abund.csv - Pocillopora SSH Occurrences per Site er Island</p> <p>Por_abund.csv - Porites SSH Occurrences per Site er Island</p> <p>mean_depth_por.csv - per site per island mean depth among Porites colonies</p> <p>mean_depth_poc.csv - per site per island mean depth among Pocillopora colonies</p>
Supporting data and codes for: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression
<p>This GitHub repository includes R codes and datasets for the paper: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression</p>
Divergent evolution between sister species of European green lizards
<p>Annotation and variant calling files (VCFs, heffas) for <em>L. viridis </em>and<em> L. bilineata.</em> The variants have been called with <em>L. viridis</em> genome as reference.</p>
FIG. 7 in A new species of Tungurictis Colbert, 1939 (Carnivora, Hyaenidae) from the middle Miocene of Junggar Basin, northwestern China and the early divergence of basal hyaenids in East Asia
FIG. 7. — Tungurictis small sp., IVPP V 11497, left dentary fragment with m1 and m2 alveolus. A, stereo photos of occlusal view; B, lingual view; C, buccal view. Scale bars: 10 mm.
FIG. 5 in A new species of Tungurictis Colbert, 1939 (Carnivora, Hyaenidae) from the middle Miocene of Junggar Basin, northwestern China and the early divergence of basal hyaenids in East Asia
FIG. 5. — Tungurictis peignei, n. sp., IVPP V 25222, holotype, right dentary with p2-m2 (A, stereo photos, occlusal view, C, lingual, and D, buccal views) and IVPP V 11493, left dentary with p2-m1 (B, stereo photos, occlusal view; E, lingual view; F, buccal views). Scale bars: 10 mm.
FIG. 4 in A new species of Tungurictis Colbert, 1939 (Carnivora, Hyaenidae) from the middle Miocene of Junggar Basin, northwestern China and the early divergence of basal hyaenids in East Asia
FIG. 4. — Tungurictis peignei, n. sp., IVPP V 25222, holotype, isolated right I3, mesial view (A), right upper canine, buccal view (B), left P1, and left maxilla with P3-4 (C, stereo photos of occlusal view; D, buccal view). Scale bar: 10 mm.
Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
<p>Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of <i>Rhagoletis pomonella </i>to their sibling species <i>R. mendax</i> that attacks blueberries. The responses of 57,857 single nucleotide polymorphisms in a diapause study on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three flies at a field site in Fennville, Michigan, USA. As anticipated, the apple race and <i>R. mendax</i> show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause experiment on <i>R. mendax</i> revealed compensatory mutations throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in <i>Rhagoletis</i>. The generality of this result is placed in the context of other similar systems.</p>
Figure 6 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 6. Relative warps analysis (RWA) of 13 dorsal cranial landmarks from 22 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 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: TM 41997ı smithersi from Pafuri) 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.g006
Figure 9 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 9. Dorsal (D), ventral (V) and lateral (L) view of bacula (tips on right) from four individuals (a–d) from Mpumalanga (Clade 1a = cohenae sp. nov.), two (e–f) from lowland sites in Mozambique (Clade 2 = mossambicus sp. nov.) and one (g) from Mt Mabu in Mozambique (Clade 1b = mabuensis sp. nov.). a = DM 11558 (Sudwala); b = DM 11620 (Barberton Tunnel; Topotype of cohenae); c = DM 11560 (Mayo); d = DM 11618 (Barberton Tunnel); e = DM 8580 (Gorongosa); f = DM 8578 (Niassa GR; Holotype of mossambicus); g = DM 10842 (Mt Mabu; Holotype of mabuensis). Bacula of Clade 1a (cohenae sp. nov.) have spatulate tip (rounded in Clades 2 (mossambicus sp. nov.) and 1b (mabuensis sp. nov.))ı typically emarginated basal portion (less so in Clades 2 and 1b) and shaft laterally compressed (cylindrical in Clades 2 and 1b) and sloping downwards in lateral view (horizontal in Clades 2 and 1b). doi:10.1371/journal.pone.0041744.g009
Figure 5 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 5. Canonical variates analysis (CVA) (a) of 10 cranial variables in five groups of the Rhinolophus hildebrandtii complex defined by molecular analysis; and PCA (b) of five cranial variables for sample in (a) with type series of hildebrandtii (''H¹'') and eloquens (''E¹'') added. Open circles = Clade 1a (= cohenae sp. nov.); closed circles = Clade 1b (= mabuensis sp. nov.); shaded circles = Clade 1d (= smithersi sp. nov.; Pafuri); asterisk enclosed in circle = Clade 1e (= smithersi sp. nov.; Zimbabwe); open squares = Clade 2 (mossambicus sp. nov.; Mozambique); shaded squares = Clade 2 (mossambicus sp. nov.; Lutopeı Zimbabwe); open diamonds = R. eloquens type series (Clade 3); crosses in circles = R. hildebrandtii type and co-type (Clade 1c). doi:10.1371/journal.pone.0041744.g005
Figure 1 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 1. Portraits of (a) Rhinolophus smithersi species novo, and (b) Rhinolophus mossambicus species novo, two of four new cryptic species described herein within the R. hildebrandtii complex. doi:10.1371/journal.pone.0041744.g001
Figure 4 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 4. Morphometric variation in a series representing the R. hildebrandtii complex from Lutope-Ngolangola, Zimbabwe: a) biplot of forearm length versus noseleaf width and b) PCA of five craniometric variables (M3M3, CM3, IOC, NW, NH) in 26 individuals of known (37 or 46 kHz) and unknown (?) frequency. Females indicated by open circlesı males by closed circles or crosses or asterisk. Voucher specimens for molecular sequencing study indicated by asterisk (Clade 1e: = smithersii sp. nov.; see Taxonomic Conclusions) and crosses (Clade 2: = mossambicus sp. nov.; see Taxonomic Conclusions). Hereafterı all individuals with a frequency of 37 kHz were assumed to belong to Clade 2 (mossambicus sp. nov.) and the 46 kHz individual was assumed to belong to Clade 1e (smithersi sp. nov.). doi:10.1371/journal.pone.0041744.g004
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
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
- Clypeus smooth (a); frons with two submedian carinae, diverging on upper frons toward lateral ocelli (b); tergite 1 of female slender, more than 1.4x longer than apically wide (c) …………………………………………………………………………E. ghesquierei Benoit, 1951 in A review of the Afrotropical Rhyssinae (Hymenoptera: Ichneumonidae) with the descriptions of five new species
- Clypeus smooth (a); frons with two submedian carinae, diverging on upper frons toward lateral ocelli (b); tergite 1 of female slender, more than 1.4x longer than apically wide (c) …………………………………………………………………………E. ghesquierei Benoit, 1951
Fig. 7 in Description of a new species of Phenacostethus (Atheriniformes: Phallostethidae) endemic to Kalimantan Selatan, Indonesian Borneo, reveals deep mtCOI divergence among miniature species
Fig. 7. Two stream habitats in Kalimantan Selatan sampled in 2007: A, Type locality of Phenacostethus sikat, the Jorong River at 20.7 m above sea level (3°58.794 S, 114°56.375 E). B, Sampanahan River at Sampanahan Hulu at 7 m above sea level (2°37.745 S, 116°11.170 E).
Fig. 6 in Description of a new species of Phenacostethus (Atheriniformes: Phallostethidae) endemic to Kalimantan Selatan, Indonesian Borneo, reveals deep mtCOI divergence among miniature species
Fig. 6. Collection localities of freshwater and coastal fishes from Kalimantan that included specimens of the genus Phenacostethus. TGK01/ TGK32 and TGK02, localities of Phenacostethus sikat. The holotype was collected at TGK01. TGK18 is the locality of Phenacostethus sp. 1, represented by one specimen (USNM 443825) distantly separated from Phe. sikat in mt COI data (see Table 4 and Discussion). Blue dots represent other localities sampled in August 2007 which included no phallostethid specimens. Yellow lines are roads. Base map from Microsoft Encarta Interactive World Atlas 2001.
Fig. 4 in Description of a new species of Phenacostethus (Atheriniformes: Phallostethidae) endemic to Kalimantan Selatan, Indonesian Borneo, reveals deep mtCOI divergence among miniature species
Fig. 4. Anterior portion of the body of specimens from which the caudal portion was removed in the field. DNA was extracted from the caudal portion for mtCOI (barcode) analysis. Above, Phenacostethus sikat, USNM 443826; below, Phenacostethus sp. 1, USNM 443825. Bars = 1 mm.
Fig. 3 in Description of a new species of Phenacostethus (Atheriniformes: Phallostethidae) endemic to Kalimantan Selatan, Indonesian Borneo, reveals deep mtCOI divergence among miniature species
Fig. 3. Phenacostethus sikat, holotype, MZB 25501, male, 13.4 mm SL. A, lateral view of head and priapium; B, ventral view of head and priapium; C, lateral view of priapium focused on brush—like seminal papilla. Phenacostethus smithi, USNM 329582, male, 16.1 mm SL. D, lateral view of head and priapium; E, ventral view of head and priapium; F, lateral view of priapium focused on ruffled seminal papilla. Bars = 1 mm.
Fig. 2. Phenacostethus sikat. A in Description of a new species of Phenacostethus (Atheriniformes: Phallostethidae) endemic to Kalimantan Selatan, Indonesian Borneo, reveals deep mtCOI divergence among miniature species
Fig. 2. Phenacostethus sikat. A, Holotype, MZB 25501, male, 13.4 mm SL. The caudal fin is damaged and incomplete. B, Paratype, USNM 443824, female, 13.8 mm SL. Bars = 1 mm.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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