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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>
Fig. 4 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 4. Pedipalps of the Leiobunum rupestre group, whole pedipalps in lateral view, single femora in medial view. — A–F. ♁♁. A–B. Leiobunum rupestre Herbst, 1799, Germany, Baden-Württemberg, CJM1954. A. Pedipalpus lateral. B. Femur medial. C–D. L. gracile Thorell, 1876, Denmark, Asp, CJM3531. C. Pedipalpus lateral. D. Femur medial. — E–F. Leiobunum apenninicum (Martens, 1969), France, Alpes- Maritimes, CJM2747. E. Pedipalpus lateral. F. Femur medial. — G–M. ♀♀. G–H. Leiobunum rupestre Herbst, 1799, Germany, Mt. Arber, CJM136. G. Pedipalpus lateral. H. Femur medial. J–K. L. gracile Thorell, 1876, Denmark, Asp, CJM3531. J. Pedipalpus lateral. K. Femur medial. L–M. L. apenninicum (Martens, 1969), France, Alpes-Maritimes, CJM2747. L. Pedipalpus lateral. M. Femur medial. Arrows indicate characters mentioned in the descriptions.
Fig. 1 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 1. Habit of Leiobunum rupestre species group. A–B. Leiobunum rupestre Herbst, 1799, Slovenia, Pohorje Mountains, resting at rock faces. A. ♁. B. ♀. C–D. Leiobunum apenninicum (Martens, 1969), Italy, Monesi di Triora, at night. C. ♁. D. ♀. E–F. Leiobunum gracile Thorell, 1876, Denmark. E. ♁. F. ♀. Photographs: A–D by A.L.Schönhofer; E–F by S. Toft, all taken in the field.
Fig. 3 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 3. Body of Leiobunum C.L. Koch, 1839, dorsal view. A–B. Leiobunum rupestre Herbst, 1799, Germany, Mt. Arber, CJM136. A. ♁. B. ♀. — C–D. Leiobunum gracile Thorell, 1876, Denmark. C. ♁, 2 km N of Skaerbaek, CJM3530. D. ♀, Asp, CJM3531. — E–F. Leiobunum apenninicum (Martens, 1969), France, Alpes-Maritimes. E. ♁, CJM1508. F. ♀, CJM2747. Drawings by K. Rehbinder.
Fig. 5. Leiobunum, male genitalia. A–C. L. rupestre Herbst, 1799 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 5. Leiobunum, male genitalia. A–C. L. rupestre Herbst, 1799, Germany, Baden-Württemberg, CJM1954. A. Ventral view. B. Lateral view. C. Cross-section. — D–F. L. gracile Thorell, 1876, Denmark, 2 km N of Skaerbaek, CJM3530. D. Ventral view. E. Lateral view. F. Cross-section. — G–J. L. apenninicum (Martens, 1969), France, Alpes-Maritimes, CJM1508. G. Ventral view. H. Lateral view. J. Cross-section. Arrows indicate the area of the respective cross-sections.
Figs 199‒204 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 199‒204. Morphology of the male genitalia for species of the subgenus Melanobombus von Dalla Torre, 1880 from the dorsal aspect, anterior at the bottom of the image, posterior at the top. 199. Bombus alagesianus Reinig, 1930 stat. rev., Georgia. 200. B. tibeticus sp. nov., China-Qinghai. 201. B. incertoides Vogt, 1911 stat. rev., Mongolia. 202. B. qilianensis sp. nov., China-Qinghai. 203. B. keriensis Morawitz, 1887, India-Kashmir. 204. B. separandus Vogt, 1909 stat. rev., Kyrgyzstan. Scale bars = 1 mm.
Figs 209–210 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 209–210. Images of queens of two cryptic species from around the western Qinghai-Tibetan plateau. 209. Bombus keriensis Morawitz, 1887 from Mt Apharwat (4000 m a.s.l.) in the Pir Panjal mountains (ML405). 210. B. separandus Vogt, 1909 stat. rev. from Nimaling plain (4800 m a.s.l.) in the Zanskar mountains (ML311). Viewed from the left lateral aspect.
Figs 12‒13 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 12‒13. Maps of sequenced samples. 12. The rufipes-group and festivus-group. 13. The rufofasciatus- group as recognised as species from the UHF-PTP analysis in Fig. 10. Keys to the coloured symbols are shown on the left (in some cases symbols on the map for one species may overlie symbols for another). Maps projected onto a sphere in ArcGIS using World_Shaded_Relief basemap © 2014 ESRI and showing boundaries between countries as recognised by the UN.
Figs 25–63 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 25–63. Simplified diagrams for the colour patterns of the hair on the dorsum for the species from the integrative analysis. The dorsum is divided into regions, each of which shows only the predominant or most apparent colour for that region using a simplified colour palette, with olive indicating a mixture of black and yellow hair, and grey indicating a mixture of black and white hair. The rufipes-group. 25. Queen, China-Taiwan. 26. Queen, China-Guangdong. 27. Worker, China-Sichuan. 28. Worker, Thailand. 29. Queen, Nepal. 30. Male, China-Sichuan. 31. Male, China-Sichuan. 32. Male, Thailand. 33. Male, Nepal. 34. Male, Nepal. 35. Queen, Indonesia-Sumatra. 36. Queen, Indonesia-Java. 37. Male, Indonesia-Java. The festivus-group. 38. Queen, Nepal. 39. Queen, China-Sichuan. 40. Worker, ChinaSichuan. 41. Worker, China-Xizang. 42. Worker, China-Yunnan. 43. Male, Nepal. 44. Male, ChinaYunnan. 45. Male, China-Yunnan. The rufofasciatus-group. 46. Queen, India-Kashmir. 47. Worker, India-Kashmir. 48. Male, India-Kashmir. 49. Male, India-Kashmir. 50. Queen, India-Arunachal Pradesh. 51. Queen, Bhutan. 52. Worker, Bhutan. 53. Worker, Bhutan. 54. Male, Bhutan. 55. Queen, India-Kashmir. 56. Queen, India-Kashmir. 57. Worker, India-Kashmir. 58. Worker, India-Kashmir. 59. Worker, IndiaKashmir. 60. Worker, Pakistan. 61. Male, India-Kashmir. 62. Male, India-Kashmir. 63. Male, Nepal.
Figs 17–20 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 17–20. Plots of (y-axis) pairwise proportion of genetic divergence between COI barcode region sequences against (x-axis) pairwise Great Circle geographical distance in km between sample sites with linear trend lines (black). 17. Genetic divergences within the candidate species for the sichelii-complex identified using Bayesian UF-PTP (Mantel r = 0.52). 18. Genetic divergences among the candidate species for the sichelii-complex identified using Bayesian UF-PTP (Mantel r = 0.21). 19. Genetic divergences within the candidate species for the keriensis-complex identified using Bayesian UF-PTP (Mantel r = 0.16). 20. Genetic divergences among the candidate species for the keriensis-complex identified using Bayesian UF-PTP (relationship not positive). For details of the measurements see the
Figs 103–138 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 103–138. Simplified diagrams for the colour patterns of the hair on the dorsum for the species from the integrative analysis. The dorsum is divided into regions, each of which shows only the predominant or most apparent colour for that region using a simplified colour palette, with olive indicating a mixture of black and yellow hair, and grey indicating a mixture of black and white hair. The tanguticus-group. 103. Worker, China-Qinghai. 104. Worker, China-Qinghai. 105. Queen, China-Qinghai. 106. Queen, China-Xizang. 107. Queen, India-Kashmir. The lapidarius-group. 108. Queen, Russia-North Ossetia. 109. Worker, Azerbaijan. 110. Queen, Georgia. 111. Male, Russia-North Ossetia. 112. Male, Russia-North Ossetia. 113. Male, Russia-North Ossetia. 114. Male, Turkey. 115. Queen, Morocco. 116. Queen, Spain. 117. Queen, Spain. 118. Queen, UK. 119. Male, Spain. 120. Male, Spain. 121. Male, UK. 122. Male, UK. The sichelii-group. 123. Queen, Iran. 124. Male, Iran. 125. Queen, India-Kashmir. 126. Queen, IndiaKashmir. 127. Male, India-Kashmir. 128. Male, India-Kashmir. 129. Queen, Iran. 130. Queen, RussiaSakha. 131. Queen, China-Sichuan. 132. Worker, China-Sichuan. 133. Queen, Mongolia. 134. Worker, Mongolia. 135. Queen, Spain. 136. Worker, Austria. 137. Male, Turkey. 138. Male, Mongolia.
Figs 207–208 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 207–208. Images of holotype workers of two new cryptic species from around the eastern QinghaiTibetan plateau. 207. Bombus tibeticus sp. nov. from near the Kunlun pass (3970 m a.s.l.) in the Kunlun mountains (ML228). 208. B. qilianensis sp. nov. from Qushiang (3370 m a.s.l.) in the Burhan Budai mountains (ML306). Viewed from the left lateral aspect.
Figs 190‒198 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 190‒198. Morphology of the male genitalia for species of the subgenus Melanobombus von Dalla Torre, 1880 from the dorsal aspect, anterior at the bottom of the image, posterior at the top. 190. Bombus friseanus Skorikov, 1933, China-Yunnan. 191. B pyrosoma Morawitz, 1890, ChinaBeijing. 192. B. formosellus (Frison, 1934), China-Taiwan. 193. B. eriophorus Klug, 1807, RussiaNorth Ossetia. 194. B. lapidarius (Linnaeus, 1758), UK. 195. B. incertus Morawitz, 1881, Turkey. 196. B. semenoviaus (Skorikov, 1914), India-Kashmir. 197. B. sichelii Radoszkowski, 1859, Austria. 198. B. ladakhensis Richards, 1928, China-Sichuan. Scale bars = 1 mm.
Figs 205–206 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 205–206. Maps of all available global records with all of the specimens examined and confirmed here. 205. Bombus richardsiellus (Tkalců, 1968). 206. B. tanguticus Morawitz, 1887. Relief map with hill shading for the region centred on Tibet with (grey lines) borders to national administration as in UN maps. Image created in ArcGIS using World_Shaded_Relief basemap © 2014 Esri.
Fig. 23. Diagram representing a in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Fig. 23. Diagram representing a corridor-dispersal model, encompassing a set of the short-distance dispersal events permitted (in either direction) between the areas defined in Table 5, based on their geographical proximity and the likely disposition of corridors with suitable habitat and favourable climates in the past.
Fig. 8 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Fig. 8. Numbers of candidate species from example Poisson-tree-process (PTP) analyses using either unfiltered (UF) or with unique haplotype filtering (UHF) from MrBayes trees from COI barcodes (y-axis) as sample sizes of selected barcoded individuals increased through time (x-axis). All analyses were rerun retrospectively with the same outgroup and model settings (see text). PTP analyses using highest Bayesian support values to fit the models (error bars for 95% confidence intervals from PTP analyses).
Figs 211–212 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 211–212. Maps of sequenced samples showing the most frequent colour patterns locally. 211. The sichelii-complex, consisting of the single polytypic species B. sichelii Radoszkowski, 1859 (inset: B. sichelii worker, China-Neimenggu, photo PW). 212. The keriensis-complex, consisting of B. alagesianus Reinig, 1930 stat. rev. (blue spots), B. tibeticus sp. nov. (dark green spots), B. incertoides Vogt, 1911 stat. rev. (light green spots), B. qilianensis sp. nov. (yellow spots), B. keriensis Morawitz, 1887 (orange spots), and B. separandus Vogt, 1909 stat. rev. (red spots) (inset: B.qilianensis sp. nov. queen, China-Sichuan, photo PW). Maps projected onto a sphere in ArcGIS using World_Shaded_Relief basemap © 2014 ESRI and showing boundaries between countries as recognised by the UN.
Fig. 22 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Fig. 22. Most likely dated phylogenetic (ultrametric) tree for the species of the subgenus Melanobombus reconstructed von Dalla Torre, 1880 with *BEAST from trees for four genes (COI, 16S, PEPCK, opsin) with B. nobilis Friese, 1905 as the outgroup (not shown), estimated as the maximum-clade-credibility tree among a sample of 10 000 species trees with a 1% burn-in out of 100 million MCMC trees. Values above the nodes are Bayesian posterior probabilities showing support for groups. Values below the nodes are estimated dates of divergence in Ma (millions of years before the present) calibrated from a molecular estimate for the date of crown divergence within the subgenus Melanobombus. Grey bars show the 95% confidence limits on the estimated dates of divergence. Species groups discussed in the text are labelled in circles: rp = rufipes-group; fs = festivus-group; rf = rufofasciatus-group; tg = tanguticus-group; la = lapidarius-group; si = sichelii-group; and ke = keriensis-group.
Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.
Data from: Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species, Crocodylus acutus and Crocodylus moreletii
<p>Hybrid zones represent natural laboratories to study gene flow, divergence and the nature of species boundaries between closely related taxa. We evaluated the level and extent of hybridization between <em>Crocodylus moreletii </em>and<em> C. acutus </em>using genetic and morphological data on 300 crocodiles from 65 localities. To our knowledge, this is the first genetic study that includes the entire historic range and sympatric zone of the two species. Contrary to expectations, Bayesian admixture proportions and maximum likelihood estimates of hybrid indexes revealed that most sampled crocodiles were admixed and that the hybrid zone is geographically extensive, extending well beyond their historical region of sympatry. We identified a few geographically isolated, non-admixed populations of both parental species. Hybrids do not appear to be F<sub>1</sub>s or recent backcrosses, but rather are more likely later-generation hybrids, suggesting that hybridization has been going on for several to many generations and is mostly the result of natural processes. <em>C. moreletii </em>is not the sister species of <em>C. acutus,</em> suggesting that the hybrid zone formed from secondary contact rather than primary divergence. Non-admixed individuals from the two species were distinguishable based on morphological characters, whereas hybrids had a complex mosaic of morphological characters that hinders identification in the wild. Very few non-admixed <em>C. acutus</em> and <em>C. moreletii</em> populations exist in the wild. Consequently, the last non-admixed <em>C. moreletii</em> populations have become critically endangered. Indeed, not only the parental species but also the naturally occurring hybrids should be considered for their potential conservation value.</p>
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