julian Kerbis | Field Museum (original) (raw)
Papers by julian Kerbis
Figure 9. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing th... more Figure 9. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing three operational taxonomic units (OTUs) of Praomys misonnei (West Africa, West Central Africa, and Central + East Africa), and two OTUs of Praomys tullbergi (males and females). The group centroids (symbols) and extreme limits of each scatter plot of points are indicated.
Figure 10. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing t... more Figure 10. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing the three operational taxonomic units (OTUs) of Praomys misonnei (West Africa, West Central Africa, and Central + East Africa). Two individuals from Nigeria were plotted on the graph. The group centroids (symbols) and extreme limits of each scatter plot of points are indicated.
Figure 8. Canonical variate axes 1 and 2 resulting from a canonical variate analysis of Praomys m... more Figure 8. Canonical variate axes 1 and 2 resulting from a canonical variate analysis of Praomys misonnei (males and females) and Praomys tullbergi (males and females). Group centroids (symbols) and extreme limits of each scatter plot of points are indicated. Only specimens previously identified by molecular analyses were included in this analysis.
Figure 6. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) cytochrome b... more Figure 6. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) cytochrome b haplotypes. Circle sizes are proportional to the number of similar haplotypes observed in the data set. Branch lengths are proportional to the number of mutations between haplotypes. See Appendix S1 for the haplotype designations.
Figure 3. Phylogeny of cytochrome b haplotypes resulting from maximum-likelihood (ML) analysis (G... more Figure 3. Phylogeny of cytochrome b haplotypes resulting from maximum-likelihood (ML) analysis (GTR + I + G model). Numbers at nodes represent ML bootstrap support (1000 replications), and Bayesian posterior probabilities.
Figure 5. Phylogeny of 16S haplotypes resulting from maximum-likelihood (ML) analysis (GTR + I + ... more Figure 5. Phylogeny of 16S haplotypes resulting from maximum-likelihood (ML) analysis (GTR + I + G model). Numbers at nodes represent ML bootstrap support (1000 replications), and Bayesian posterior probabilities.
Figure 1. Map showing the 40 sites yielding the specimens of Praomys tullbergi and Praomys misonn... more Figure 1. Map showing the 40 sites yielding the specimens of Praomys tullbergi and Praomys misonnei that were included in the molecular analyses. For the names of the localities, see Table 1. Forests are indicated in light grey (adapted from Mayaux et al., 2004).
Additional file 2: Table S1. Summary statistics of linear cranial measurements and centroid size ... more Additional file 2: Table S1. Summary statistics of linear cranial measurements and centroid size (CS) of species the non-Ethiopian L. flavopunctatus members. The values represent the 95% confidence interval mean | standard deviation | minimum–maximum values. Table S2. Summary of multivariate pairwise differences between the non-Ethiopian L. flavopunctatus members based on linear measurements and geometric craniodental landmarks inferred using permutational multivariate analysis of variance. Values represent pairwise PerMANOVAs between clade pairs as post hoc tests with the upper matrix showing the F values and the lower matrix showing the Bonferroni-corrected p values (statistically significant values are in bold). The test of PerMANOVA showed overall significant skull differences between clades in both the linear dataset (Total sum of squares: 35510; Within-group sum of squares: 29300; F: 15.13, p: 0.0001) and geometric dataset (Total sum of squares:0.3591; Within-group sum of squa...
Maximum likelihood gene tree inferred for cyt-b using IQ-TREE that includes two sequences of R. g... more Maximum likelihood gene tree inferred for cyt-b using IQ-TREE that includes two sequences of R. gorongosae deposited in GenBank [12; indicated by red font] and five specimens newly sequenced for cyt-b in this study (indicated by blue font). DM14815 is included twice in the tree (both the GenBank sequence and a newly generated sequence from this study). Nodal support is indicated above branches. Museum acronyms are defined in Additional file 1. (PDF 533 kb)
Maximum likelihood phylogeny of 350 mitochondrial cytochrome-b sequences of Rhinolophus. The phyl... more Maximum likelihood phylogeny of 350 mitochondrial cytochrome-b sequences of Rhinolophus. The phylogeny was inferred in IQ-TREE and its topology was very similar to the Bayesian phylogeny calculated in MRBAYES. Filled black circles on nodes denote bootstrap values (BS) ≥ 70% and Bayesian posterior probabilities (PP) ≥ 0.95, left-half-filled circles indicate BS ≥ 70% and PP
Uncorrected cyt-b p-distances among (below diagonal) and within (numbers on diagonal) African Rhi... more Uncorrected cyt-b p-distances among (below diagonal) and within (numbers on diagonal) African Rhinolophus clades calculated in MEGA X 10.0.5 [36]. (XLS 46 kb)
Primer information for regions amplified in the current study. (DOCX 18 kb)
List of specimens used in genetic analyses of Rhinolophus. (XLSX 55 kb)
Figure 4. Schematic representation of the distribution of Praomys tullbergi and Praomys misonnei,... more Figure 4. Schematic representation of the distribution of Praomys tullbergi and Praomys misonnei, and of the four P. misonnei populations (clades I–IV) resulting from phylogenetic analyses. Potential extrinsic barriers to gene flow (rivers) are indicated.
![Research paper thumbnail of Morphological and genetic characterization of Mount Kenya brush-furred rats (Lophuromys Peters 1874); relevance to taxonomy and ecology [Erratum: Apr. 2020, v.65(2), p.401]](https://attachments.academia-assets.com/112886286/thumbnails/1.jpg)
](Mammal research, 2020
The aim of this study was to determine some morphological characters and genetic relations of ind... more The aim of this study was to determine some morphological characters and genetic relations of indeterminate green bean accessions having different seed coat color collected from the Black Sea region of Turkey. In this research, a total of 39 green bean accessions and one kidney bean accession consisting of different main seed coat colors (white, black, yellow, green, brown, red, and dark red) and mixed seed coat colors were used. Plants were produced under greenhouse conditions for morphological characterization. We used 43 morphological characters described by UPOV for indeterminate green bean. In molecular analysis, the sequence-related amplified polymorphism (SRAP) marker system was used. A total of 21 primer combinations produced 138 bands. DNA band profiles were analyzed by NTSYS and a UPGMA dendrogram was generated. The total polymorphism rate was found to be 85.5%. According to research results, indeterminate green bean accessions showed a high level of morphological variation; however, narrow genetic diversity was detected based on molecular analysis.
Journal of Biogeography, Aug 11, 2015
AimThis study aims to reconstruct the evolutionary history of the African rodent genus Malacomys ... more AimThis study aims to reconstruct the evolutionary history of the African rodent genus Malacomys and to identify factors driving diversification within this genus.LocationAfrican tropical lowland forest.MethodsAnalyses were based on sampling representatives from most of the known geographical range of the genus. We assessed genetic structure and historical biogeography using a combination of mitochondrial and nuclear markers. Morphological differences between lineages were analysed using a geometric morphometric approach.ResultsThree species of Malacomys are recognized within the genus. Two are endemic to West Africa, and one is endemic to Central Africa. Our analyses reveal a strong phylogeographical structure with 13 lineages, most of them allopatric or parapatric. A complex biogeographical history, including dispersal–vicariance events, explains the current genetic structure of Malacomys. Discrete divergence events within the genus are dated to the mid‐Pliocene (3.7 Ma, 95% range: 2.4–5.2 Ma) and the Pleistocene (less than 1.9 Ma, with most events less than 1 Ma). Morphological variation is partly congruent with genetic structure and may indicate local adaptations.Main conclusionsClimatic oscillations, which led to periodic fragmentation of the forest habitat, seem to be the major driver of diversification within this genus. Our results support the existence of multiple small, rather than a few large, forest refugia during glacial maxima. Rivers have played a significant role in shaping boundaries of several regional haplogroups, either by promoting diversification or by preventing secondary contact between previously isolated lineages.
BMC Ecology and Evolution
Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been diff... more Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. Results The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subge...
Figure 7. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) 16S haplotyp... more Figure 7. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) 16S haplotypes. Circle sizes are proportional to the number of similar haplotypes observed in the data set. Branch lengths are proportional to the number of mutations between haplotypes. See Appendix S1 for the haplotype designations.
Figure 2. Schematic drawings of a skull (in dorsal, ventral, and lateral views) and mandibule of ... more Figure 2. Schematic drawings of a skull (in dorsal, ventral, and lateral views) and mandibule of of Praomys, showing the 21 craniodental variables recorded in this study (see the Material and methods section for the definitions of these measurements).
Figure 9. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing th... more Figure 9. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing three operational taxonomic units (OTUs) of Praomys misonnei (West Africa, West Central Africa, and Central + East Africa), and two OTUs of Praomys tullbergi (males and females). The group centroids (symbols) and extreme limits of each scatter plot of points are indicated.
Figure 10. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing t... more Figure 10. Canonical variate axes 1 and 2 resulting from a canonical variate analysis comparing the three operational taxonomic units (OTUs) of Praomys misonnei (West Africa, West Central Africa, and Central + East Africa). Two individuals from Nigeria were plotted on the graph. The group centroids (symbols) and extreme limits of each scatter plot of points are indicated.
Figure 8. Canonical variate axes 1 and 2 resulting from a canonical variate analysis of Praomys m... more Figure 8. Canonical variate axes 1 and 2 resulting from a canonical variate analysis of Praomys misonnei (males and females) and Praomys tullbergi (males and females). Group centroids (symbols) and extreme limits of each scatter plot of points are indicated. Only specimens previously identified by molecular analyses were included in this analysis.
Figure 6. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) cytochrome b... more Figure 6. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) cytochrome b haplotypes. Circle sizes are proportional to the number of similar haplotypes observed in the data set. Branch lengths are proportional to the number of mutations between haplotypes. See Appendix S1 for the haplotype designations.
Figure 3. Phylogeny of cytochrome b haplotypes resulting from maximum-likelihood (ML) analysis (G... more Figure 3. Phylogeny of cytochrome b haplotypes resulting from maximum-likelihood (ML) analysis (GTR + I + G model). Numbers at nodes represent ML bootstrap support (1000 replications), and Bayesian posterior probabilities.
Figure 5. Phylogeny of 16S haplotypes resulting from maximum-likelihood (ML) analysis (GTR + I + ... more Figure 5. Phylogeny of 16S haplotypes resulting from maximum-likelihood (ML) analysis (GTR + I + G model). Numbers at nodes represent ML bootstrap support (1000 replications), and Bayesian posterior probabilities.
Figure 1. Map showing the 40 sites yielding the specimens of Praomys tullbergi and Praomys misonn... more Figure 1. Map showing the 40 sites yielding the specimens of Praomys tullbergi and Praomys misonnei that were included in the molecular analyses. For the names of the localities, see Table 1. Forests are indicated in light grey (adapted from Mayaux et al., 2004).
Additional file 2: Table S1. Summary statistics of linear cranial measurements and centroid size ... more Additional file 2: Table S1. Summary statistics of linear cranial measurements and centroid size (CS) of species the non-Ethiopian L. flavopunctatus members. The values represent the 95% confidence interval mean | standard deviation | minimum–maximum values. Table S2. Summary of multivariate pairwise differences between the non-Ethiopian L. flavopunctatus members based on linear measurements and geometric craniodental landmarks inferred using permutational multivariate analysis of variance. Values represent pairwise PerMANOVAs between clade pairs as post hoc tests with the upper matrix showing the F values and the lower matrix showing the Bonferroni-corrected p values (statistically significant values are in bold). The test of PerMANOVA showed overall significant skull differences between clades in both the linear dataset (Total sum of squares: 35510; Within-group sum of squares: 29300; F: 15.13, p: 0.0001) and geometric dataset (Total sum of squares:0.3591; Within-group sum of squa...
Maximum likelihood gene tree inferred for cyt-b using IQ-TREE that includes two sequences of R. g... more Maximum likelihood gene tree inferred for cyt-b using IQ-TREE that includes two sequences of R. gorongosae deposited in GenBank [12; indicated by red font] and five specimens newly sequenced for cyt-b in this study (indicated by blue font). DM14815 is included twice in the tree (both the GenBank sequence and a newly generated sequence from this study). Nodal support is indicated above branches. Museum acronyms are defined in Additional file 1. (PDF 533 kb)
Maximum likelihood phylogeny of 350 mitochondrial cytochrome-b sequences of Rhinolophus. The phyl... more Maximum likelihood phylogeny of 350 mitochondrial cytochrome-b sequences of Rhinolophus. The phylogeny was inferred in IQ-TREE and its topology was very similar to the Bayesian phylogeny calculated in MRBAYES. Filled black circles on nodes denote bootstrap values (BS) ≥ 70% and Bayesian posterior probabilities (PP) ≥ 0.95, left-half-filled circles indicate BS ≥ 70% and PP
Uncorrected cyt-b p-distances among (below diagonal) and within (numbers on diagonal) African Rhi... more Uncorrected cyt-b p-distances among (below diagonal) and within (numbers on diagonal) African Rhinolophus clades calculated in MEGA X 10.0.5 [36]. (XLS 46 kb)
Primer information for regions amplified in the current study. (DOCX 18 kb)
List of specimens used in genetic analyses of Rhinolophus. (XLSX 55 kb)
Figure 4. Schematic representation of the distribution of Praomys tullbergi and Praomys misonnei,... more Figure 4. Schematic representation of the distribution of Praomys tullbergi and Praomys misonnei, and of the four P. misonnei populations (clades I–IV) resulting from phylogenetic analyses. Potential extrinsic barriers to gene flow (rivers) are indicated.
Mammal research, 2020
The aim of this study was to determine some morphological characters and genetic relations of ind... more The aim of this study was to determine some morphological characters and genetic relations of indeterminate green bean accessions having different seed coat color collected from the Black Sea region of Turkey. In this research, a total of 39 green bean accessions and one kidney bean accession consisting of different main seed coat colors (white, black, yellow, green, brown, red, and dark red) and mixed seed coat colors were used. Plants were produced under greenhouse conditions for morphological characterization. We used 43 morphological characters described by UPOV for indeterminate green bean. In molecular analysis, the sequence-related amplified polymorphism (SRAP) marker system was used. A total of 21 primer combinations produced 138 bands. DNA band profiles were analyzed by NTSYS and a UPGMA dendrogram was generated. The total polymorphism rate was found to be 85.5%. According to research results, indeterminate green bean accessions showed a high level of morphological variation; however, narrow genetic diversity was detected based on molecular analysis.
Journal of Biogeography, Aug 11, 2015
AimThis study aims to reconstruct the evolutionary history of the African rodent genus Malacomys ... more AimThis study aims to reconstruct the evolutionary history of the African rodent genus Malacomys and to identify factors driving diversification within this genus.LocationAfrican tropical lowland forest.MethodsAnalyses were based on sampling representatives from most of the known geographical range of the genus. We assessed genetic structure and historical biogeography using a combination of mitochondrial and nuclear markers. Morphological differences between lineages were analysed using a geometric morphometric approach.ResultsThree species of Malacomys are recognized within the genus. Two are endemic to West Africa, and one is endemic to Central Africa. Our analyses reveal a strong phylogeographical structure with 13 lineages, most of them allopatric or parapatric. A complex biogeographical history, including dispersal–vicariance events, explains the current genetic structure of Malacomys. Discrete divergence events within the genus are dated to the mid‐Pliocene (3.7 Ma, 95% range: 2.4–5.2 Ma) and the Pleistocene (less than 1.9 Ma, with most events less than 1 Ma). Morphological variation is partly congruent with genetic structure and may indicate local adaptations.Main conclusionsClimatic oscillations, which led to periodic fragmentation of the forest habitat, seem to be the major driver of diversification within this genus. Our results support the existence of multiple small, rather than a few large, forest refugia during glacial maxima. Rivers have played a significant role in shaping boundaries of several regional haplogroups, either by promoting diversification or by preventing secondary contact between previously isolated lineages.
BMC Ecology and Evolution
Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been diff... more Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. Results The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subge...
Figure 7. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) 16S haplotyp... more Figure 7. Minimum spanning network of Praomys misonnei (A) and Praomys tullbergi (B) 16S haplotypes. Circle sizes are proportional to the number of similar haplotypes observed in the data set. Branch lengths are proportional to the number of mutations between haplotypes. See Appendix S1 for the haplotype designations.
Figure 2. Schematic drawings of a skull (in dorsal, ventral, and lateral views) and mandibule of ... more Figure 2. Schematic drawings of a skull (in dorsal, ventral, and lateral views) and mandibule of of Praomys, showing the 21 craniodental variables recorded in this study (see the Material and methods section for the definitions of these measurements).