Phylogenetic Comparative Approach Research Articles

From bridewealth to dowry? : A bayesian estimation of ancestral states of marriage transfers in Indo-European groups.

Significant amounts of wealth have been exchanged as part of marriage settlements throughout history. Although various models have been proposed for interpreting these practices, their development over time has not been investigated systematically. In this paper we use a Bayesian MCMC phylogenetic comparative approach to reconstruct the evolution of two forms of wealth transfers at marriage, dowry and bridewealth, for 51 Indo-European cultural groups. Results indicate that dowry is more likely to have been the ancestral practice, and that a minimum of four changes to bridewealth is necessary to explain the observed distribution of the two states across the cultural groups.

RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales

RNA editing in plant mitochondria alters the RNA sequence by converting C-to-U or U-to-C at a specific site. We investigated the requirement for RNA editing in the complete genomic sequences of the gene encoding the cytochrome oxidase subunit III ( cox3) and the ribosomal protein S13 ( rps13) in 59 closely related species within the Asparagales and Liliales (monocots). To obtain a comprehensive picture of the degree of variation in editing we explored the non-synonymous RNA editing sites within the newly sequenced cox3 and rps13 genes by a comparative phylogenetic approach. RNA editing is predicted to occur in all the surveyed species, but to different extents. Zero to one non-synonymous editing site is inferred in the cox3 mRNA in species from Amaryllidaceae and Iridaceae. No RNA editing of rps13 mRNAs is required in Amaryllidaceae, because all respective genomic sequences resemble the edited version of the mRNAs of other analysed land plants. The observed absence of cox3 and rps13 RNA editing in Iridaceae and Amaryllidaceae and the striking RNA editing reduction of ccb2 in the latter family is likely generated by recombination and reverse transcription mediated events involving edited mitochondrial transcripts.

Biogeographic, environmental, and phylogenetic influences on reproductive traits in subtropical forest trees, South Africa

The distribution of subtropical forests in South Africa is largely a consequence of climatic change during the Quaternary period. We gathered data for 195 canopy tree species from Afrotemperate, scarp, and coastal forests in KwaZulu‐Natal, South Africa and assessed patterns in reproductive traits using a comparative phylogenetic approach. The overlap in species composition among the forest types reflected the geographic position and colonisation history of the forests. Despite a high degree of phylogenetic conservatism in reproductive traits, there were differences in their expression among forest types. Afrotemperate forests had a higher incidence of wind pollination, consistent with the steep topography, seasonally dry environment, and limited resource availability in the habitat. Scarp forests had more dry brown fruits with abiotic (explosive and wind) dispersal. Coastal forests had the most species with fleshy fruits, zoochory, and large seeds, all traits that may have facilitated the colonisation or persistence of species in this more recent and dynamic community. Since many suites of traits occur together in diverse phylogenetic lines, they represent adaptive complexes that are influenced by biogeography and environmental conditions. Overall, this study demonstrates that biogeography, environmental factors, and phylogenetic history all influence the distribution of reproductive traits in these forest communities.

The evolution of reproductive and genomic diversity in ray‐finned fishes: insights from phylogeny and comparative analysis

Collectively, ray‐finned fishes (Actinopterygii) display far more diversity in many reproductive and genomic features than any other major vertebrate group. Recent large‐scale comparative phylogenetic analyses have begun to reveal the evolutionary patterns and putative causes for much of this diversity. Several such recent studies have offered clues to how different reproductive syndromes evolved in these fishes, as well as possible physiological and genomic triggers. In many cases, repeated independent origins of complex reproductive strategies have been uncovered, probably reflecting convergent selection operating on common suites of underlying genes and hormonal controls. For example, phylogenetic analyses have uncovered multiple origins and predominant transitional pathways in the evolution of alternative male reproductive tactics, modes of parental care and mechanisms of sex determination. They have also shown that sexual selection in these fishes is repeatedly associated with particular reproductive strategies. Collectively, studies on reproductive and genomic diversity across the Actinopterygii illustrate both the strengths and the limitations of comparative phylogenetic approaches on large taxonomic scales.

Latitudinal gradients in abundance, and the causes of rarity in the tropics: a test using Australian honeyeaters (Aves: Meliphagidae)

Several studies have uncovered interspecific latitudinal gradients in abundance (population density) such that tropical species tend to be, on average, less abundant than species at higher latitudes. The causes of this relationship remain poorly studied, in contrast to the relative wealth of literature examining the relationship to latitude of other variables such as range size and body mass. We used a cross-species phylogenetic comparative approach and a spatial approach to examine three potential determining factors (distribution, reproductive output and climate) that might explain why abundance correlates with latitude, using data from 54 species of honeyeaters (Meliphagidae) in woodland environments in eastern Australia. There is a strong positive correlation between mean abundance and latitude in these birds. Reproductive output (clutch size) was positively linked to both abundance and latitude, but partial correlation analysis revealed that clutch size is not related to abundance once the effects of latitude are removed. A subsequent multiple regression model that also considered range size, clutch size and body mass showed that latitude is the only strong predictor of abundance in honeyeaters. In the separate spatial analysis, the climatic variables that we considered (temperature, rainfall and seasonality) were all strongly linked to latitude, but none served as a better predictor of abundance than latitude per se, either individually or collectively. The most intriguing result of our analyses was that the cross-species latitudinal pattern in abundance was not evident within species. This suggests an intrinsic cause of the pattern of 'rarity in the tropics' in Australian honeyeaters. We suggest that evolutionary age may provide a key to understanding patterns of abundance in these birds.

Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs

Abstract A neurological method for assessment of nasal cavity homologies in extant archosaurs is extended to lambeosaurine hadrosaurids (Dinosauria: Ornithischia) to test functional hypotheses associated with their hypertrophied nasal passages and highly derived cranial crests. The olfactory system and associated cranial nerve pathways that have consistent relationships to soft tissue divisions of the nasal cavity are reconstructed in lambeosaurines on the basis of new paleoneurological data and a comparative phylogenetic approach. The new model of the lambeosaurine olfactory system and nasal cavity shows that a significant portion of nasal cavity proper was located outside the crest cavities and that the primary olfactory region was located rostromedial to the orbits. All available data indicate that the evolutionary hypertrophy of the nasal cavity occurred predominantly within the non-olfactory nasal vestibule, and that crest development was not causally associated with olfaction. The high level of inte...

A PHYLOGENETIC PERSPECTIVE ON THE EVOLUTION OF CHROMATIC ULTRAVIOLET PLUMAGE COLORATION IN GRACKLES AND ALLIES (ICTERIDAE)

Plumage traits have been studied intensely for more than a century, especially bright and exaggerated plumage. A large body of evidence across a range of avian taxa supports sexual selection as a major evolutionary force acting on plumage colors. The discovery of ultraviolet (UV) coloration in avian plumage resulted in the extension of sexual selection hypotheses to explain the evolution of potential UV plumage traits. However, there have been no comparative evolutionary studies elucidating the origin of UV signals in birds. Here, I used a comparative phylogenetic approach to investigate the evolution of chromatic UV plumage colors in the grackles-and-allies clade of the New World blackbirds (Icteridae). On the basis of reflectance data collected from museum study skins, I have determined that UV plumage signals have evolved multiple times from an ancestral condition that lacked UV plumage signals, with very few unambiguous reversals. Although UV plumage has evolved in both males and females, there have been significantly more evolutionary changes in male UV plumage characters. Concentrated changes tests and correlations of independent contrasts reveal evidence for sexual selection of some male UV plumage characters, as well as an increase in UV plumage coloration for species found in open habitats. These results support the use of objective assessments of avian colors (i.e. spectrophotometry) to properly interpret patterns of plumage evolution generally, and they suggest the need for behavioral studies on the function of chromatic UV signals in several blackbird species. Una Perspectiva Filogenética sobre la Evolución de la Coloración Ultravioleta en los Changos y Chamones (Icteridae)

A Phylogenetic Perspective on the Evolution of Chromatic Ultraviolet Plumage Coloration in Grackles and Allies (Icteridae)

AbstractPlumage traits have been studied intensely for more than a century, especially bright and exaggerated plumage. A large body of evidence across a range of avian taxa supports sexual selection as a major evolutionary force acting on plumage colors. The discovery of ultraviolet (UV) coloration in avian plumage resulted in the extension of sexual selection hypotheses to explain the evolution of potential UV plumage traits. However, there have been no comparative evolutionary studies elucidating the origin of UV signals in birds. Here, I used a comparative phylogenetic approach to investigate the evolution of chromatic UV plumage colors in the grackles-and-allies clade of the New World blackbirds (Icteridae). On the basis of reflectance data collected from museum study skins, I have determined that UV plumage signals have evolved multiple times from an ancestral condition that lacked UV plumage signals, with very few unambiguous reversals. Although UV plumage has evolved in both males and females, there have been significantly more evolutionary changes in male UV plumage characters. Concentrated changes tests and correlations of independent contrasts reveal evidence for sexual selection of some male UV plumage characters, as well as an increase in UV plumage coloration for species found in open habitats. These results support the use of objective assessments of avian colors (i.e. spectrophotometry) to properly interpret patterns of plumage evolution generally, and they suggest the need for behavioral studies on the function of chromatic UV signals in several blackbird species.Una Perspectiva Filogenética sobre la Evolución de la Coloración Ultravioleta en los Changos y Chamones (Icteridae)

The evolutionary history of Cys-tRNACys formation.

The recent discovery of an alternate pathway for indirectly charging tRNA(Cys) has stimulated a re-examination of the evolutionary history of Cys-tRNA(Cys) formation. In the first step of the pathway, O-phosphoseryl-tRNA synthetase charges tRNA(Cys) with O-phosphoserine (Sep), a precursor of the cognate amino acid. In the following step, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep to Cys in a tRNA-dependent reaction. The existence of such a pathway raises several evolutionary questions, including whether the indirect pathway is a recent evolutionary invention, as might be implied from its localization to the Euryarchaea, or, as evidence presented here indicates, whether this pathway is more ancient, perhaps already in existence at the time of the last universal common ancestral state. A comparative phylogenetic approach is used, combining evolutionary information from protein sequences and structures, that takes both the signature of horizontal gene transfer and the recurrence of the full canonical phylogenetic pattern into account, to document the complete evolutionary history of cysteine coding and understand the nature of this process in the last universal common ancestral state. Resulting from the historical study of tRNA(Cys) aminoacylation and the integrative perspective of sequence, structure, and function are 3D models of O-phosphoseryl-tRNA synthetase and SepCysS, which provide experimentally testable predictions regarding the identity and function of key active-site residues in these proteins. The model of SepCysS is used to suggest a sulfhydrylation reaction mechanism, which is predicted to occur at the interface of a SepCysS dimer.

Melanin-Based Black Plumage Coloration is Related to Reproductive Investment in Cardueline Finches

AbstractAvian color ornaments produced by different mechanisms (i.e., melanin, carotenoid, and structural colors) can communicate different sets of information due to differences in their condition or developmental constraints. Although this suggests that different color signals should be analyzed separately, few comparative studies have focused on specific types of coloration. In cardueline finches, interspecific variation in overall plumage brightness (which integrates all types of coloration) was previously shown to be affected by sexual selection and to covary with fecundity and parental care. Using a phylogenetic comparative approach, we extended this line of research and tested whether a specific component of plumage ornamentation, the melanin-based black frontal coloration of finches, showed a similar association with reproductive effort. We found that the extent of male melanization and melanin dichromatism increased in species with reduced clutch sizes, whereas female melanization was negatively correlated with incubation length. These results remained significant when we controlled for the effects of several ecological variables, and were also consistent between two alternative multivariate model-selection approaches. Our results are consistent with the hypothesis that interspecific variation in melanization may be related to fecundity and parental care through trade-offs between investment in sexual signals and parental efforts.

Allometric scaling of flight energetics in Panamanian orchid bees: a comparative phylogenetic approach

The relationship between body size and flight energetics was studied in the clade of tropical orchid bees, in order to investigate energy metabolism and evolution. Body mass, which varied from 47 to 1065 mg, was found to strongly affect hovering flight mass-specific metabolic rates, which ranged from 114 ml CO(2) h(-1) g(-1) in small species to 37 ml CO(2) h(-1) g(-1) in large species. Similar variation of wingbeat frequency in hovering flight occurred among small to large species, and ranged from 250 to 86 Hz. The direct relationship between such traits was studied by the comparative method of phylogenetically independent contrasts (PIC), using a new molecular phylogeny generated from the cytochrome b gene partial sequences. We found wingbeat frequency variation is satisfactorily explained by variation in wing loading, after corrections for body mass and phylogeny. The correlated evolution of mass-specific metabolic rate, wingbeat frequency and wing loading was also revealed after correcting for phylogeny and body mass. Further, the effect of body size on flight energetics can be understood in terms of a relationship between wing form and kinematics, which directly influence and explain the scaling of metabolic rate in this group of bees.

PHYLOGENETIC PERSPECTIVES IN THE EVOLUTION OF PARENTAL CARE IN RAY-FINNED FISHES

Among major vertebrate groups, ray-finned fishes (Actinopterygii) collectively display a nearly unrivaled diversity of parental care activities. This fact, coupled with a growing body of phylogenetic data for Actinopterygii, makes these fishes a logical model system for analyzing the evolutionary histories of alternative parental care modes and associated reproductive behaviors. From an extensive literature review, we constructed a supertree for ray-finned fishes and used its phylogenetic topology to investigate the evolution of several key reproductive states including type of parental care (maternal, paternal, or biparental), internal versus external fertilization, internal versus external gestation, nest construction behavior, and presence versus absence of sexual dichromatism (as an indicator of sexual selection). Using a comparative phylogenetic approach, we critically evaluate several hypotheses regarding evolutionary pathways toward parental care. Results from maximum parsimony reconstructions indicate that all forms of parental care, including paternal, biparental, and maternal (both external and internal to the female reproductive tract) have arisen repeatedly and independently during ray-finned fish evolution. The most common evolutionary transitions were from external fertilization directly to paternal care and from external fertilization to maternal care via the intermediate step of internal fertilization. We also used maximum likelihood phylogenetic methods to test for statistical correlations and contingencies in the evolution of pairs of reproductive traits. Sexual dichromatism and nest construction proved to be positively correlated with the evolution of male parental care in species with external fertilization. Sexual dichromatism was also positively correlated with female-internal fertilization and gestation. No clear indication emerged that female-only care or biparental care were evolutionary outgrowths of male-only care, or that biparental care has been a common evolutionary stepping stone between paternal and maternal care. Results are discussed in the context of prior thought about the evolution of alternative parental care modes in vertebrates.

MELANIN-BASED BLACK PLUMAGE COLORATION IS RELATED TO REPRODUCTIVE INVESTMENT IN CARDUELINE FINCHES

Abstract Avian color ornaments produced by different mechanisms (i.e., melanin, carotenoid, and structural colors) can communicate different sets of information due to differences in their condition or developmental constraints. Although this suggests that different color signals should be analyzed separately, few comparative studies have focused on specific types of coloration. In cardueline finches, interspecific variation in overall plumage brightness (which integrates all types of coloration) was previously shown to be affected by sexual selection and to covary with fecundity and parental care. Using a phylogenetic comparative approach, we extended this line of research and tested whether a specific component of plumage ornamentation, the melanin-based black frontal coloration of finches, showed a similar association with reproductive effort. We found that the extent of male melanization and melanin dichromatism increased in species with reduced clutch sizes, whereas female melanization was negatively...

PHYLOGENETIC PERSPECTIVES IN THE EVOLUTION OF PARENTAL CARE IN RAY-FINNED FISHES

Among major vertebrate groups, ray-finned fishes (Actinopterygii) collectively display a nearly unrivaled diversity of parental care activities. This fact, coupled with a growing body of phylogenetic data for Actinopterygii, makes these fishes a logical model system for analyzing the evolutionary histories of alternative parental care modes and associated reproductive behaviors. From an extensive literature review, we constructed a supertree for ray-finned fishes and used its phylogenetic topology to investigate the evolution of several key reproductive states including type of parental care (maternal, paternal, or biparental), internal versus external fertilization, internal versus external gestation, nest construction behavior, and presence versus absence of sexual dichromatism (as an indicator of sexual selection). Using a comparative phylogenetic approach, we critically evaluate several hypotheses regarding evolutionary pathways toward parental care. Results from maximum parsimony reconstructions indicate that all forms of parental care, including paternal, biparental, and maternal (both external and internal to the female reproductive tract) have arisen repeatedly and independently during ray-finned fish evolution. The most common evolutionary transitions were from external fertilization directly to paternal care and from external fertilization to maternal care via the intermediate step of internal fertilization. We also used maximum likelihood phylogenetic methods to test for statistical correlations and contingencies in the evolution of pairs of reproductive traits. Sexual dichromatism and nest construction proved to be positively correlated with the evolution of male parental care in species with external fertilization. Sexual dichromatism was also positively correlated with female-internal fertilization and gestation. No clear indication emerged that female-only care or biparental care were evolutionary outgrowths of male-only care, or that biparental care has been a common evolutionary stepping stone between paternal and maternal care. Results are discussed in the context of prior thought about the evolution of alternative parental care modes in vertebrates.

Large Subunit Mitochondrial rRNA Secondary Structures and Site-Specific Rate Variation in Two Lizard Lineages

A phylogenetic-comparative approach was used to assess and refine existing secondary structure models for a frequently studied region of the mitochondrial encoded large subunit (16S) rRNA in two large lizard lineages within the Scincomorpha, namely the Scincidae and the Lacertidae. Potential pairings and mutual information were analyzed to identify site interactions present within each lineage and provide consensus secondary structures. Many of the interactions proposed by previous models were supported, but several refinements were possible. The consensus structures allowed a detailed analysis of rRNA sequence evolution. Phylogenetic trees were inferred from Bayesian analyses of all sites, and the topologies used for maximum likelihood estimation of sequence evolution parameters. Assigning gamma-distributed relative rate categories to all interacting sites that were homologous between lineages revealed substantial differences between helices. In both lineages, sites within helix G2 were mostly conserved, while those within helix E18 evolved rapidly. Clear evidence of substantial site-specific rate variation (covarion-like evolution) was also detected, although this was not strongly associated with specific helices. This study, in conjunction with comparable findings on different, higher-level taxa, supports the ubiquitous nature of site-specific rate variation in this gene and justifies the incorporation of covarion models in phylogenetic inference.

The comparative method in conservation biology

The phylogenetic comparative approach is a statistical method for analyzing correlations between traits across species. Whilst it has revolutionized evolutionary biology, can it work for conservation biology? Although it is correlative, advocates of the comparative method hope that it will reveal general mechanisms in conservation, provide shortcuts for prioritizing conservation research, and enable us to predict which species will experience (or create) problems in the future. Here, we ask whether these stated management goals are being achieved. We conclude that comparative methods are stimulating research into the ecological mechanisms underlying conservation, and are providing information for preemptive screening of problem species. But comparative analyses of extinction risk to date have tended to be too broad in scope to provide shortcuts to conserving particular endangered species. Correlates of vulnerability to conservation problems are often taxon, region and threat specific, so models must be narrowly focused to be of maximum practical use.

A comparative phylogenetic approach for dating whole genome duplication events.

Whole genome duplications have played a major role in determining the structure of eukaryotic genomes. Current evidence revealing large blocks of duplicated chromatin yields new insights into the evolutionary history of species, but also presents a major challenge for researchers attempting to utilize comparative genomics techniques. Understanding the timing of duplication events relative to divergence among taxa is critical to accurate and comprehensive cross-species comparisons. We describe a large-scale approach to estimate the timing of duplication events in a phylogenetic context. The methodology has been previously utilized for analysis of Arabidopsis and Saccharomyces duplication events. This new implementation provides a more flexible and reusable framework for these analyses. Scripts written in the Python programming language drive a number of freely available bioinformatics programs, creating a no-cost tool for researchers. The usefulness of the approach is demonstrated through genome-scale analysis of Arabidopsis and Oryza (rice) duplications. Software and documentation are freely available from http://plantgenome.agtec.uga.edu/bioinformatics/dating/

Mitochondrial DNA reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages

Freshwater catchments of south-east Australia possess generally rich and diverse macroinvertebrate faunas, although the genetic structuring of these assemblages is poorly known. In this study, we assessed mitochondrial phylogenetic structure within four genera of macroinvertebrates from the Sydney Water Supply Catchment, south-east Australia: Euastacus (parastacid crayfish), Cheumatopsyche (hydropsychid caddisflies), Atalophlebia (leptophlebiid mayflies) and Paratya (atyid shrimp), with a view to prioritising areas of high diversity for future conservation efforts. We found extremely divergent (≈4–19%) cytochrome c oxidase subunit I (COI) lineages within all surveyed groups, many of which corresponded to recognised taxa, although there was also evidence of cryptic species within three genera; Euastacus, Atalophlebia and Paratya. Distributions of these three genera were associated with high altitude streams, above dam impoundments. Our results have important implications for management of the Sydney Water Supply Catchment. Future disturbance in this region is likely to be high and priority should be directed towards preserving the diversity of fauna in these upland areas. This comparative phylogenetic approach may have value as a means to focus and direct conservation efforts in other areas supporting high biodiversity.

Biological correlates of extinction risk in bats.

We investigated patterns and processes of extinction and threat in bats using a multivariate phylogenetic comparative approach. Of nearly 1,000 species worldwide, 239 are considered threatened by the International Union for Conservation of Nature and Natural Resources (IUCN) and 12 are extinct. Small geographic ranges and low wing aspect ratios are independently found to predict extinction risk in bats, which explains 48% of the total variance in IUCN assessments of threat. The pattern and correlates of extinction risk in the two bat suborders are significantly different. A higher proportion (4%) of megachiropteran species have gone extinct in the last 500 years than microchiropteran bats (0.3%), and a higher proportion is currently at risk of extinction (Megachiroptera: 34%; Microchiroptera: 22%). While correlates of microchiropteran extinction risk are the same as in the order as a whole, megachiropteran extinction is correlated more with reproductive rate and less with wing morphology. Bat extinction risk is not randomly distributed phylogenetically: closely related species have more similar levels of threat than would be expected if extinction risk were random. Given the unbalanced nature of the evolutionary diversification of bats, it is probable that the amount of phylogenetic diversity lost if currently threatened taxa disappear may be greater than in other clades with numerically more threatened species.

RECONSTRUCTING THE EVOLUTION OF COMPLEX BIRD SONG IN THE OROPENDOLAS

Abstract The elaborate songs of songbirds are frequent models for investigating the evolution of animal signals. However, few previous studies have attempted to reconstruct historical changes in song evolution using a phylogenetic comparative approach. In particular, no comparative studies of bird song have used a large number of vocal characters and a well-supported, independently derived phylogeny. We identified 32 features in the complex vocal displays of male oropendolas (genera Psarocolius, Gymnostinops, and Ocyalus) that are relatively invariant within taxa and mapped these characters onto a robust molecular phylogeny of the group. Our analysis revealed that many aspects of oropendola song are surprisingly evolutionarily conservative and thus are potentially useful characters for reconstructing historical patterns. Of the characters that varied among taxa, nearly two thirds (19 of 29) showed no evidence of evolutionary convergence or reversal when mapped onto the tree, which was reflected in a high overall consistency index (CI = 0.78) and retention index (RI = 0.88). Some reconstructed patterns provided evidence of selection on these signals. For example, rapid divergence of the songs of the Montezuma oropendola, Gymnostinops montezuma, from those of closely related taxa suggests the recent influence of strong sexual selection. In general, our results provide insights into the mode of vocal evolution in songbirds and suggest that complex vocalizations can provide information about phylogeny. Based on this evidence, we use song characters to estimate the phylogenetic affinities of three oropendola taxa for which molecular data are not yet available.