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18 results for “continuous phylogeography”
Continuous phylogeography analysis of Rift Valley fever virus (RVFV) in Africa and the Arabian Peninsula
<p>Spatiotemporal-explicit Bayesian phylogenetic trees and MCMC log files for Rift Valley fever virus large, medium and non-structural genetic sequences generated by BEAST v1.10</p> <ol> <li>Log files (logs.zip)</li> <li>Tree files (trees.zip)</li> </ol>
Data from: Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae)
Current population genetic models fail to cope with genetic differentiation for species with large, contiguous and heterogeneous distribution. We show that in such a case, genetic differentiation can be predicted at equilibrium by circuit theory, where conductance corresponds to abundance in species distribution models (SDM). Circuit-SDM approach was used for the phylogeographic study of the lepidopteran cereal stemborer Busseola fusca Füller (Noctuidae) across sub-Saharan Africa. Species abundance was surveyed across its distribution range. SDM models were optimized and selected by cross validation. Relationship between observed matrices of genetic differentiation between individuals, and matrices of resistance distance was assessed through Mantel tests and redundancy discriminant analyses (RDA). A total of 628 individuals from 130 localities in 17 countries were genotyped at 7 microsatellite loci. Six population clusters were found based on a Bayesian analysis. The eastern margin of Dahomey Gap between East and West Africa was the main factor of genetic differentiation. The SDM projections at present, last interglacial and last glacial maximum periods were used for estimation of circuit resistance between locations of genotyped individuals. For all periods of time, when using either all individuals or only East-African individuals, partial Mantel r and RDA analyses conditioning on geographic distance were found significant. Under future projections (year 2080), partial r and RDA significance were different. From this study, it is concluded that analytical solutions provided by circuit theory are useful for the evolutionary management of populations and for phylogeographic analysis when coalescence times are not accessible by approximate Bayesian simulations.
Data from: Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae)
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Figures 6-15 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 6-15 Shell variability in Monachacantiana s.l. CAN-5 from Piastra (FGC 41563) (6, 7), Foce di Pianza (FGC 41565) (8, 9) and Campo Cecina (FGC 41564) (10–12); CAN-6 from Campagrina (FGC 40322) (13–15).
Figures 42- 43 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 42- 43 Principal component analysis (PCA) and Redundancy analysis (RDA) with lineage applied to the original genitalia matrix (42) and Z-matrix (shape-related) (43).
Figures 35-41 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 35-41 Genitalia (proximal parts excluded) (35), internal structure of distal genitalia (36) and transverse sections of medial epiphallus (37, 39), basal and apical penial papilla (38, 40, 41) of Monachacantiana s.l. CAN-6 from Campagrina (FGC 40322).
Figures 30-34 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 30-34 Genitalia (proximal parts excluded) (30), transverse sections of medial epiphallus (31, 32) and basal and apical penial papilla (33, 34) of Monachacantiana s.l. CAN-5 Campo Cecina (FGC 41564).
Figures 25-29 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 25-29 Genitalia (proximal parts excluded) (25), internal structure of distal genitalia (26), transverse sections of medial epiphallus (27) and basal and apical penial papilla (28, 29) of Monachacantiana s.l. CAN-5 from Foce di Pianza (FGC 41565).
Figures 19-24 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 19-24 Genitalia (proximal parts excluded) (19), internal structure of distal genitalia (20), transverse sections of medial epiphallus (21, 22) and basal and apical penial papilla (23, 24) of Monachacantiana s.l. CAN-5 from Piastra (FGC 41563).
Figures 16- 17 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 16- 17 Principal component analysis (PCA) and Redundancy analysis (RDA) with lineage constraint applied to the original shell matrix (16) and Z-matrix (shape-related) (17).
Figures 45-47 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figures 45-47 Syntypes and original labels of Monacha species from Apuan Alps established by Mabille (1881). Helixapuanica (45) (MHNG-MOLL-115981), Helixardesa (46) (MHNG-MOLL-115982), Helixsobara (47) (MHNG-MOLL-116022) (by courtesy of E. Tardy, Muséum d'histoire naturelle, Genève, Switzerland).
Figure 4 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figure 4 The median-joining haplotype network for COI haplotypes of Monachacantiana s.l. The colours of the circles indicate Monacha species, and their size is proportional to haplotype frequencies. Small black circles are hypothetical missing intermediates. The numbers next to the branches indicate distance between taxa expressed in numbers of mutant positions. Only numbers above 10 are indicated.
Figure 44 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figure 44 Box plots for genitalia characters of the seven Monacha clades investigated. The lower and upper limits of the rectangular boxes indicate the 25th to 75th percentile range, and the horizontal line within the boxes is the median (50th percentile).
Figure 3 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figure 3 Bayesian 50% majority-rule consensus tree of the combined data set of COI and 16SrDNA haplotypes, and H3 and ITS2 common sequences (see Table 4). Posterior probabilities (left) and bootstrap support above 50% from ML analysis (right) are indicated next to the branches. Bootstrap analysis was run with 1000 replicates (Felsenstein 1985). The tree was rooted with M.cartusiana and M.parumcincta combined sequences obtained from GenBank (Table 4).
Figure 2 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figure 2 Maximum Likelihood (ML) tree of combined H3 and ITS2 common sequences of Monachacantiana s.l. (see Table 4). Numbers next to the branches indicate bootstrap support above 50% calculated for 1000 replicates (Felsenstein 1985). The tree was rooted with M.cartusiana and M.parumcincta combined sequences obtained from GenBank (Table 4).
Figure 18 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figure 18 Box plots for shell characters of the seven Monacha clades investigated. The lower and upper limits of the rectangular boxes indicate the 25th to 75th percentile range, and the horizontal line within the boxes is the median (50th percentile).
Figure 1 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figure 1 Maximum Likelihood (ML) tree of combined COI and 16SrDNA haplotypes of Monachacantiana s.l. (see Table 4). Numbers next to the branches indicate bootstrap support above 50% calculated for 1000 replicates (Felsenstein 1985). The tree was rooted with M.cartusiana and M.parumcincta combined sequences obtained from GenBank (Table 4).
Figure 5 from: Pieńkowska JR, Manganelli G, Giusti F, Barbato D, Hallgass A, Lesicki A (2019) Exploration of phylogeography of Monacha cantiana s.l. continues: the populations of the Apuan Alps (NW Tuscany, Italy) (Eupulmonata, Stylommatophora, Hygromiidae). ZooKeys 814: 115-149. https://doi.org/10.3897/zookeys.814.31583
Figure 5 Haplotype network for 16SrDNA of Monachacantiana s.l. Other explanations as in Figure 4.
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Allen Brain Atlas
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