Differences in the limits and range of aerobic activity levels between endotherms and ectotherms ... more Differences in the limits and range of aerobic activity levels between endotherms and ectotherms remain poorly understood, though such differences help explain basic differences in species' lifestyles (e.g. movement patterns, feeding modes and interaction rates). We compare the limits and range of aerobic activity in endotherms (birds and mammals) and ectotherms (fishes, reptiles and amphibians) by evaluating the body mass-dependence of VO<sub>2</sub> max, aerobic scope and heart mass in a phylogenetic context based on a newly constructed vertebrate supertree. Contrary to previous work, results show no significant differences in the body mass scaling of minimum and maximum oxygen consumption rates with body mass within endotherms or ectotherms. For a given body mass, resting rates and maximum rates were 24-fold and 30-fold lower, respectively, in ectotherms than endotherms. Factorial aerobic scope ranged from five to eight in both groups, with scope in endotherms showing a modest body mass-dependence. Finally, maximum consumption rates and aerobic scope were positively correlated with residual heart mass. Together, these results quantify similarities and differences in the potential for aerobic activity among ectotherms and endotherms from diverse environments. They provide insights into the models and mechanisms that may underlie the body mass-dependence of oxygen consumption.
Molecular Phylogenetics and Evolution, Feb 1, 2015
Saxifragaceae (Saxifragales) contain approximately 640 species and 33 genera, about half of which... more Saxifragaceae (Saxifragales) contain approximately 640 species and 33 genera, about half of which are monotypic. Due to factors such as morphological stasis, convergent morphological evolution, and disjunct distributions, relationships within Saxifragaceae have historically been troublesome. The family occurs primarily in mountainous regions of the Northern Hemisphere, with the highest generic and species diversity in western North America, but disjunct taxa are known from southern South America. Here, we integrate broad gene (56 loci) and taxon (223 species) sampling strategies, both the most comprehensive to date within Saxifragaceae, with fossil calibrations and geographical distribution data to address relationships, divergence times, and historical biogeography among major lineages of Saxifragaceae. Two previously recognized main clades, the heucheroids (eight groups+Saniculiphyllum) and saxifragoids (Saxifraga s.s.), were re-affirmed by our phylogenetic analyses. Relationships among the eight heucheroid groups, as well as the phylogenetic position of Saniculiphyllum within the heucheroids, were resolved with mostly high support. Divergence time estimates indicate that Saxifragaceae began to diversify ca. 38.37 million years ago (Mya; 95% HPD=30.99-46.11Mya) in the Mid-Late Eocene, and that the two major lineages, the heucheroids and saxifragoids, began to diversify approximately 30.04Mya (95% HPD=23.87-37.15Mya) and 30.85 Mya (95% HPD=23.47-39.33Mya), respectively. We reconstructed ancestral geographic areas using statistical dispersal-vicariance (S-DIVA). These analyses indicate several radiations within Saxifragaceae: one in eastern Asia and multiple radiations in western North America. Our results also demonstrate that large amounts of sequence data coupled with broad taxon sampling can help resolve clade relationships that have thus far seemed intractable.
Mathematical Biology and Bioinformatics, Nov 16, 2022
Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwid... more Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwide. This study presents the first natural hierarchical classification of Coronaviridae. We also demonstrate a “one-step” solution to incorporate the principles of binomial (binary) nomenclature into taxonomy of Coronaviridae. We strongly support the complete rejection of the non-taxonomic category “virus” in any future taxonomic study in virology. This will aid future recognition of numerous virus species, particularly in the currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host.
A new species — Elytrigia fursaevii Laktionov, Tzvelev et Mavrodiev from the Lower Volga Region i... more A new species — Elytrigia fursaevii Laktionov, Tzvelev et Mavrodiev from the Lower Volga Region is described. Its distinctions from the related E. repens (L.) Nevski are specified.
Tragopogon (Asteraceae) includes two recently and repeatedly formed allopolyploids, T. mirus and ... more Tragopogon (Asteraceae) includes two recently and repeatedly formed allopolyploids, T. mirus and T. miscellus, both of which formed in western North America following the human‐mediated introduction of three diploids from Europe: T. dubius, T. porrifolius, and T. pratensis. We recently investigated the genetics of the introduction history to North America of T. dubius, the shared parent of both allopolyploids. Here, we investigate the introduction of T. pratensis into North America, the second diploid parent of T. miscellus. Using ITS sequence data, we found that T. pratensis as currently defined in the narrow sense is polyphyletic and comprises at least four different major ITS types in its native range. Of these native range ITS patterns, two have been introduced from Europe into North America and now occur widely across Canada and the U.S.A. Although the allotetraploid T. miscellus formed multiple times in western North America, only one of these ITS types was involved in the recurrent formations. These results for T. pratensis parallel our findings for T. dubius and further suggest that not all genotypes of these two species may be able to participate in the formation of allopolyploids. Our phylogenetic analyses reveal that several entities traditionally considered part of T. pratensis in the narrow sense are genetically distinct and mark unique lineages that may ultimately merit recognition as separate species. This proclivity for genetically distinct entities (potential cryptic species) within species recognized based on morphology appears common in Tragopogon. To unravel the complexities of what is referred to as “T. pratensis”, more intensive phylogenetic analyses involving many more samples from across the geographic range of the species are required, as are detailed assessments of taxonomy, morphology, and cytology.
The possibility of undertaking matrix/optimization-free cladistic analysis is one of the most int... more The possibility of undertaking matrix/optimization-free cladistic analysis is one of the most interesting ideas to emerge in the last few decades from within the field of systematics, particularly in the development of cladistics. The purpose of this paper is to design further opportunities and prospects made possible by eliminating the matrix as the primary source of data representation. The main focus of this paper is to outline a supertree approach that, if combined with the methodology of three-taxon statement analysis (3TA), may be seen as a powerful heuristic alternative to the application of conventional matrix/optimization-based methods used for the analysis of systematic data, and which currently forms the mainstream of contemporary phylogenetics. Using the average consensus technique as an example, we demonstrate explicitly that methods of construction of supertrees may be applied to the array of three-taxon statements (3TS), especially if the latter are represented initially as minimal trees, not as binary matrices, as was originally proposed. The 3TA-average consensus procedure recognizes solely ‘reversal’-based clades and is also free from the potential issues of 3TA, such as the data distortion due to inability to handle putative reversals. Thus the main benefit of this new approach over the traditional one is its accuracy and advantages when implementing the Hennigian views on the cladistic analysis that states that all characters must be a priori polarized before the best fitting tree is found. We also found that the average consensus technique (as well as other median supertree calculation techniques) is purely typological and we stressed that this simple point had never been mentioned before. We proposed that the average consensus of 3TSs (as well as any median consensus of 3TSs) may be viewed as a median type and the extended procedure of the traditional 3TA may be treated as a typology of the relations. The connection between median type and phylogeny may be established only indirectly. The heuristic scientific typology may be derived within a completely metaphysics-free context. Goethe’s idea of “Urphenomenon” and Max Weber’s “Ideal Types” are mentioned as examples of heuristic metaphysical-free typological frameworks.
Differences in the limits and range of aerobic activity levels between endotherms and ectotherms ... more Differences in the limits and range of aerobic activity levels between endotherms and ectotherms remain poorly understood, though such differences help explain basic differences in species' lifestyles (e.g. movement patterns, feeding modes and interaction rates). We compare the limits and range of aerobic activity in endotherms (birds and mammals) and ectotherms (fishes, reptiles and amphibians) by evaluating the body mass-dependence of VO<sub>2</sub> max, aerobic scope and heart mass in a phylogenetic context based on a newly constructed vertebrate supertree. Contrary to previous work, results show no significant differences in the body mass scaling of minimum and maximum oxygen consumption rates with body mass within endotherms or ectotherms. For a given body mass, resting rates and maximum rates were 24-fold and 30-fold lower, respectively, in ectotherms than endotherms. Factorial aerobic scope ranged from five to eight in both groups, with scope in endotherms showing a modest body mass-dependence. Finally, maximum consumption rates and aerobic scope were positively correlated with residual heart mass. Together, these results quantify similarities and differences in the potential for aerobic activity among ectotherms and endotherms from diverse environments. They provide insights into the models and mechanisms that may underlie the body mass-dependence of oxygen consumption.
Molecular Phylogenetics and Evolution, Feb 1, 2015
Saxifragaceae (Saxifragales) contain approximately 640 species and 33 genera, about half of which... more Saxifragaceae (Saxifragales) contain approximately 640 species and 33 genera, about half of which are monotypic. Due to factors such as morphological stasis, convergent morphological evolution, and disjunct distributions, relationships within Saxifragaceae have historically been troublesome. The family occurs primarily in mountainous regions of the Northern Hemisphere, with the highest generic and species diversity in western North America, but disjunct taxa are known from southern South America. Here, we integrate broad gene (56 loci) and taxon (223 species) sampling strategies, both the most comprehensive to date within Saxifragaceae, with fossil calibrations and geographical distribution data to address relationships, divergence times, and historical biogeography among major lineages of Saxifragaceae. Two previously recognized main clades, the heucheroids (eight groups+Saniculiphyllum) and saxifragoids (Saxifraga s.s.), were re-affirmed by our phylogenetic analyses. Relationships among the eight heucheroid groups, as well as the phylogenetic position of Saniculiphyllum within the heucheroids, were resolved with mostly high support. Divergence time estimates indicate that Saxifragaceae began to diversify ca. 38.37 million years ago (Mya; 95% HPD=30.99-46.11Mya) in the Mid-Late Eocene, and that the two major lineages, the heucheroids and saxifragoids, began to diversify approximately 30.04Mya (95% HPD=23.87-37.15Mya) and 30.85 Mya (95% HPD=23.47-39.33Mya), respectively. We reconstructed ancestral geographic areas using statistical dispersal-vicariance (S-DIVA). These analyses indicate several radiations within Saxifragaceae: one in eastern Asia and multiple radiations in western North America. Our results also demonstrate that large amounts of sequence data coupled with broad taxon sampling can help resolve clade relationships that have thus far seemed intractable.
Mathematical Biology and Bioinformatics, Nov 16, 2022
Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwid... more Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwide. This study presents the first natural hierarchical classification of Coronaviridae. We also demonstrate a “one-step” solution to incorporate the principles of binomial (binary) nomenclature into taxonomy of Coronaviridae. We strongly support the complete rejection of the non-taxonomic category “virus” in any future taxonomic study in virology. This will aid future recognition of numerous virus species, particularly in the currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host.
A new species — Elytrigia fursaevii Laktionov, Tzvelev et Mavrodiev from the Lower Volga Region i... more A new species — Elytrigia fursaevii Laktionov, Tzvelev et Mavrodiev from the Lower Volga Region is described. Its distinctions from the related E. repens (L.) Nevski are specified.
Tragopogon (Asteraceae) includes two recently and repeatedly formed allopolyploids, T. mirus and ... more Tragopogon (Asteraceae) includes two recently and repeatedly formed allopolyploids, T. mirus and T. miscellus, both of which formed in western North America following the human‐mediated introduction of three diploids from Europe: T. dubius, T. porrifolius, and T. pratensis. We recently investigated the genetics of the introduction history to North America of T. dubius, the shared parent of both allopolyploids. Here, we investigate the introduction of T. pratensis into North America, the second diploid parent of T. miscellus. Using ITS sequence data, we found that T. pratensis as currently defined in the narrow sense is polyphyletic and comprises at least four different major ITS types in its native range. Of these native range ITS patterns, two have been introduced from Europe into North America and now occur widely across Canada and the U.S.A. Although the allotetraploid T. miscellus formed multiple times in western North America, only one of these ITS types was involved in the recurrent formations. These results for T. pratensis parallel our findings for T. dubius and further suggest that not all genotypes of these two species may be able to participate in the formation of allopolyploids. Our phylogenetic analyses reveal that several entities traditionally considered part of T. pratensis in the narrow sense are genetically distinct and mark unique lineages that may ultimately merit recognition as separate species. This proclivity for genetically distinct entities (potential cryptic species) within species recognized based on morphology appears common in Tragopogon. To unravel the complexities of what is referred to as “T. pratensis”, more intensive phylogenetic analyses involving many more samples from across the geographic range of the species are required, as are detailed assessments of taxonomy, morphology, and cytology.
The possibility of undertaking matrix/optimization-free cladistic analysis is one of the most int... more The possibility of undertaking matrix/optimization-free cladistic analysis is one of the most interesting ideas to emerge in the last few decades from within the field of systematics, particularly in the development of cladistics. The purpose of this paper is to design further opportunities and prospects made possible by eliminating the matrix as the primary source of data representation. The main focus of this paper is to outline a supertree approach that, if combined with the methodology of three-taxon statement analysis (3TA), may be seen as a powerful heuristic alternative to the application of conventional matrix/optimization-based methods used for the analysis of systematic data, and which currently forms the mainstream of contemporary phylogenetics. Using the average consensus technique as an example, we demonstrate explicitly that methods of construction of supertrees may be applied to the array of three-taxon statements (3TS), especially if the latter are represented initially as minimal trees, not as binary matrices, as was originally proposed. The 3TA-average consensus procedure recognizes solely ‘reversal’-based clades and is also free from the potential issues of 3TA, such as the data distortion due to inability to handle putative reversals. Thus the main benefit of this new approach over the traditional one is its accuracy and advantages when implementing the Hennigian views on the cladistic analysis that states that all characters must be a priori polarized before the best fitting tree is found. We also found that the average consensus technique (as well as other median supertree calculation techniques) is purely typological and we stressed that this simple point had never been mentioned before. We proposed that the average consensus of 3TSs (as well as any median consensus of 3TSs) may be viewed as a median type and the extended procedure of the traditional 3TA may be treated as a typology of the relations. The connection between median type and phylogeny may be established only indirectly. The heuristic scientific typology may be derived within a completely metaphysics-free context. Goethe’s idea of “Urphenomenon” and Max Weber’s “Ideal Types” are mentioned as examples of heuristic metaphysical-free typological frameworks.
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