Pollination syndromes and the origins of floral traits

BACKGROUND

A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes.

SCOPE

The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century.

CONCLUSIONS

The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.

Steinernema shori n. sp., a new entomopathogenic nematode (Nematoda: Steinernematidae) from India

In this study, morphological and molecular features were used to identify a new Steinernema sp. from Chhattisgarh, India. Morphological and molecular features provide evidence for placing the new species into the "bicornutum" clade. The new species is characterized by the following morphological features: infective juveniles with a body length of 587 (494-671) μm; a distance from the anterior end to excretory pore of 46 (43-50) μm; a distance from anterior end to nerve ring of 72 μm (61-85 μm); and E% of 88 (77-97). The first-generation males are characterised by 27 genital papillae and very short spicules, with a length of 61 μm (53-67) μm. The SW% and GS% ratio of S. shori n. sp. are 139 (107-190) and 75 (62-90), respectively. The new species is further characterized by sequences of the internal transcribed spacer and partial 28S regions of the ribosomal DNA. Phylogenetic analyses show that S. shori n. sp. is most closely related to S. abbasi, S. kandii, and S. yirgalemense.

A new Bolitoglossa (Amphibia, Caudata, Plethodontidae) from the Cordillera Oriental of Colombia

A new salamander species of the genus Bolitoglossa is here described from the cloud forests of the western slopes of the Cordillera Oriental of Colombia, in the Cundinamarca department. The most salient characters of this new species are its numerous maxillary and vomerine teeth, its moderate webbing on hands and feet, its short and robust tail, and its chromatic variation. Based on molecular analyses this new species is assigned to the adspersa species group and its status established as the sister species of B.adspersa, with which it was previously confused. Lastly, the distribution, natural history, and conservation status of the new species are discussed.

Multigene Sequence-Based and Phenotypic Characterization Reveals the Occurrence of a Novel Entomopathogenic Nematode Species, Steinernema anantnagense n. sp

Three entomopathogenic nematode populations were isolated from agricultural fields in the Anantnag district of Jammu and Kashmir (India). Sequences of multiple gene regions and phenotypic features show that they are conspecific and represent a novel species. Molecular and morphological features provided evidence for placing the new species into the "Kushidai" clade. Within this clade, analysis of sequence data of the internal transcribed spacer (ITS) gene, the D2D3 region of the 28S rRNA gene, the mitochondrial cytochrome oxidase I (mtCOI) gene, and the mitochondrial 12S (mt12S) gene depicted the novel species as a distinctive entity closely related to Steinernema akhursti, S. kushidai, and S. populi. Phylogenetic analyses also show that the new species is a sister species to S. akhursti, and these two species are closely related to S. kushidai and S. populi. Additionally, the new species does not mate or produce fertile progeny with any of the closely related species, reinforcing its uniqueness from a biological species concept standpoint. The new species is further characterized by the third-stage infective juveniles with almost straight bodies (0.7-0.8 mm length), poorly developed stoma and pharynx, and conoid-elongate tail (49-66 µm) with hyaline posterior part. Adult females are characterized by short and conoid tails bearing a short mucron in the first generation and long conoid tails with thin mucron in the second generation. Adult males have ventrally curved spicules in both generations. Moreover, the first-generation male has rounded manubrium, fusiform gubernaculum, conoid and slightly ventrally curved tails with minute mucron, and the second generation has rhomboid manubrium anteriorly ventrad bent, and tails with long and robust mucron. The morphological, morphometrical, molecular, and phylogenetic analyses support the new species status of this nematode, which is hereby described as Steinernema anantnagense n. sp. The bacterial symbiont associated with S. anantnagense n. sp. represents a novel species, closely related to Xenorhabdus japonica. These findings shed light on the diversity of entomopathogenic nematodes and their symbiotic bacteria, providing valuable information for future studies in this field.

Corrigendum: Genotype-phenotype correlations within the Geodermatophilaceae

[This corrects the article DOI: 10.3389/fmicb.2022.975365.].

Genotype-phenotype correlations within the Geodermatophilaceae

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO₂ fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.

Steinernema populi n. sp. (Panagrolaimomorpha, Steinernematidae), a new entomopathogenic nematode species from China

Steinernema populi n. sp. was recovered by baiting from beneath poplar trees in China. Morphological and molecular features provided evidence for placing the new species into the Kushidai clade. The new species is characterized by the following morphological features: third-stage infective juveniles (IJ) with a body length of 1095 (973-1172) μm, a distance from the anterior end to excretory pore of 77 (70-86) μm and a tail length of 64 (55-72) μm. The Body length/Tail length (c) ratio and Anterior end to Excretory pore/ Tail length × 100 (E%) of S. populi n. sp. are substantially greater than those of all other 'Feltiae-Kushidai-Monticolum' group members. The first-generation males can be recognized by a spicule length of 66 (57-77) μm and a gubernaculum length of 46 (38-60) μm. The new species is further characterized by sequences of the internal transcribed spacer and partial 28S regions of the ribosomal DNA. Phylogenetic analyses show that Steinernema akhursti and Steinernema kushidai are the closest relatives to S. populi n. sp.

Mitochondrial Phylogenomics of Tenthredinidae (Hymenoptera: Tenthredinoidea) Supports the Monophyly of Megabelesesinae as a Subfamily

Tenthredinidae represents one of the external feeders of the most diverse superfamily, Tenthredinoidea, with diverse host plant utilization. In this study, four complete mitochondrial genomes (mitogenomes), those of Cladiucha punctata, Cladiucha magnoliae, Megabeleses magnoliae, and Megabeleses liriodendrovorax, are newly sequenced and comparatively analyzed with previously reported tenthredinid mitogenomes. The close investigation of mitogenomes and the phylogeny of Tenthredinidae leads us to the following conclusions: The subfamilial relationships and phylogenetic placements within Tenthredinidae are mostly found to be similar to the previously suggested phylogenies. However, the present phylogeny supports the monophyly of Megabelesesinae as a subfamily, with the sister-group placement of Cladiucha and Megabeleses outside of Allantinae. The occurrence of the same type of tRNA rearrangements (MQI and ANS1ERF) in the mitogenomes of Megabelesesinae species and the presence of apomorphic morphological characters also provide robust evidence for this new subfamily. The divergence and diversification times of the subfamilies appear to be directly related to colonization of the flowering plants following the Early Cretaceous. The origin time and diversification patterns of Megabelesesinae were also well matched with the divergence times of their host plants from Magnoliaceae.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus, is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus. In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus, G. brasiliensis, G. soli, G. taihuensis, and G. terrae. Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.

MACROEVOLUTIONARY PATTERNS OF MORPHOLOGICAL DIVERSIFICATION AMONG PARASITIC FLATWORMS (PLATYHELMINTHES: CERCOMERIA)

Patterns of parasite morphological diversification were investigated using a morphological data base for the parasitic platyhelminths comprising 1,459 characters analyzed using phylogenetic systematic methods. Only 10.8% of the 1,882 character transformations are losses, casting doubt on views that parasites are secondarily simplified and exhibit degenerate evolution. Chi-squared analysis indicates that character loss in the Digenea and Monogenea occurs in proportion to total change and is disproportionately lower within the Eucestoda. In the Digenea fewer female characters and more male characters have been lost than expected by the total number of characters in that group, and more male and more nonreproductive characters have been lost in proportion to their distribution across groups. In the Monogenea fewer nonreproductive and more larval characters have been lost than expected within the group, and female character loss is high relative to other groups. In the Eucestoda fewer female and more larval characters have been lost than expected within the group, whereas loss of male and nonreproductive character is low, and loss of larval characters is high, compared to the other groups. Patterns of character loss result partially from characters that show repeated (homoplasious) loss in different groups. High consistency index and low homoplasy slope ratio values indicate that the parasitic platyhelminths show unusually low levels of homoplasy, casting doubt on views that parasite morphology is unusually adaptively plastic. Homoplasy within the monogeneans occurs in proportion to overall character change, is slightly higher than expected in the digeneans, and is much lower than expected within the eucestodes. Homoplasy occurs less often than expected in larval characters, and more often than expected in nonreproductive characters in the Digenea. Monogeneans show more homoplasy than expected for larval characters both within and among groups. Eucestodes show fewer homoplasious male and nonreproductive, and more homoplasious larval, characters than expected within the group, and higher homoplasy in larval characters and lower homoplasy in female and nonreproductive characters among groups.

Analysis of the complete plastomes of three species of Membranoptera (Ceramiales, Rhodophyta) from Pacific North America

Next generation sequence data were generated and used to assemble the complete plastomes of the holotype of Membranoptera weeksiae, the neotype (designated here) of M. tenuis, and a specimen examined by Kylin in making the new combination M. platyphylla. The three plastomes were similar in gene content and length and showed high gene synteny to Calliarthron, Grateloupia, Sporolithon, and Vertebrata. Sequence variation in the plastome coding regions were 0.89% between M. weeksiae and M. tenuis, 5.14% between M. weeksiae and M. platyphylla, and 5.18% between M. tenuis and M. platyphylla. We were unable to decipher the complete mitogenomes of the three species due to low coverage and structural problems; however, we assembled and analyzed, the cytochrome oxidase I, II, and III loci and found that M. weeksiae and M. tenuis differed in sequence by 1.3%, M. weeksiae and M. platyphylla by 8.4%, and M. tenuis and M. platyphylla by 8.1%. Evaluation of standard marker genes indicated that sequences from the rbcL, RuBisCO spacer, and CO1 genes closely approximated the pair-wise genetic distances observed between the plastomes of the three species of Membranoptera. A phylogenetic tree based on rbcL sequences showed that M. tenuis and M. weeksiae were sister taxa. Short rbcL sequences were obtained from type specimens of M. dimorpha, M. multiramosa, and M. edentata and confirmed their conspecificity with M. platyphylla. The data support the recognition of three species of Membranoptera occurring south of Alaska: M. platyphylla, M. tenuis, and M. weeksiae.

An Evolutionary Framework for Understanding the Origin of Eukaryotes

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution

Molecular biology has provided a rich dataset to develop hypotheses of nervous system evolution. The startling patterning similarities between distantly related animals during the development of their central nervous system (CNS) have resulted in the hypothesis that a CNS with a single centralized medullary cord and a partitioned brain is homologous across bilaterians. However, the ability to precisely reconstruct ancestral neural architectures from molecular genetic information requires that these gene networks specifically map with particular neural anatomies. A growing body of literature representing the development of a wider range of metazoan neural architectures demonstrates that patterning gene network complexity is maintained in animals with more modest levels of neural complexity. Furthermore, a robust phylogenetic framework that provides the basis for testing the congruence of these homology hypotheses has been lacking since the advent of the field of 'evo-devo'. Recent progress in molecular phylogenetics is refining the necessary framework to test previous homology statements that span large evolutionary distances. In this review, we describe recent advances in animal phylogeny and exemplify for two neural characters-the partitioned brain of arthropods and the ventral centralized nerve cords of annelids-a test for congruence using this framework. The sequential sister taxa at the base of Ecdysozoa and Spiralia comprise small, interstitial groups. This topology is not consistent with the hypothesis of homology of tripartitioned brain of arthropods and vertebrates as well as the ventral arthropod and rope-like ladder nervous system of annelids. There can be exquisite conservation of gene regulatory networks between distantly related groups with contrasting levels of nervous system centralization and complexity. Consequently, the utility of molecular characters to reconstruct ancestral neural organization in deep time is limited.

Osteology of Priocharax and remarkable developmental truncation in a miniature Amazonian fish (Teleostei: Characiformes: Characidae)

Establishing phylogenetic relationships of miniature fishes is challenging in taxa with developmental truncation. Within the Characiformes, developmental truncation appears to be relatively rare, with the Neotropical genus Priocharax being an example. Priocharax includes three miniature species among the smallest of the order and has been hypothesized to belong to the Heterocharacinae. The pronounced reduction in its skeleton, however, prevented a clearer evaluation of its relationships. The present detailed osteological study was designed to address this question and revealed that 21 bones are absent and nine other skeletal structures are simplified in Priocharax when compared to other characids. Comparison of the skeleton of adult Priocharax with early developmental stages of other characids demonstrated that most of the absences and simplifications can be interpreted as developmental truncations. The most striking developmental truncations are in the pectoral girdle, in which the endoskeleton remains entirely cartilaginous. Other interesting truncations are in the ethmoid region of the skull, infraorbital series, and Weberian apparatus, in which the claustrum is absent. Our study also revealed some unusual sexual dimorphisms in the pelvic girdle. Two cladistic analyses were performed to assess the relationships of Priocharax within the Heterocharacinae. The first consisted of a traditional analysis in which all absences and reductions of Priocharax were coded in the same way as in the remaining taxa. This resulted in three equally most parsimonious topologies, all of which have Priocharax as the most basal taxon of the Heterocharacinae. The second analysis incorporated ontogenetic information, and most absences and reductions of Priocharax were reinterpreted as apomorphic conditions and thus, coded differently from similar conditions in outgroups. This resulted in a single phylogenetic hypothesis with Priocharax and Gnathocharax as sister groups based on seven synapomorphies. Our approach demonstrates the importance of developmental studies to better understand morphological evolution of miniaturized, truncated taxa, and to generate hypotheses of their relationships.

Phylogeny, classification, and fruit evolution of the species-rich Neotropical bellflowers (Campanulaceae: Lobelioideae)

•

PREMISE OF THE STUDY

The species-rich Neotropical genera Centropogon, Burmeistera, and Siphocampylus represent more than half of the ∼1200 species in the subfamily Lobelioideae (Campanulaceae). They exhibit remarkable morphological variation in floral morphology and habit. Limited taxon sampling and phylogenetic resolution, however, obscures our understanding of relationships between and within these genera and underscores our uncertainty of the systematic value of fruit type as a major diagnostic character.•

METHODS

We inferred a phylogeny from five plastid DNA regions (rpl32-trnL, ndhF-rpl32, rps16-trnK, trnG-trnG-trns, rbcL) using maximum-likelihood and Bayesian inference. Ancestral character reconstructions were applied to infer patterns of fruit evolution.•

KEY RESULTS

Our results demonstrate that the majority of species in the genera Centropogon, Burmeistera, and Siphocampylus together form a primarily mainland Neotropical clade, collectively termed the "centropogonids." Caribbean Siphocampylus, however, group with other Caribbean lobelioid species. We find high support for the monophyly of Burmeistera and the polyphyly of Centropogon and mainland Siphocampylus. The ancestral fruit type of the centropogonids is a capsule; berries have evolved independently multiple times.•

CONCLUSIONS

Our plastid phylogeny greatly improves the phylogenetic resolution within Neotropical Lobelioideae and highlights the need for taxonomic revisions in the subfamily. Inference of ancestral character states identifies a dynamic pattern of fruit evolution within the centropogonids, emphasizing the difficulty of diagnosing broad taxonomic groups on the basis of fruit type. Finally, we identify that the centropogonids, Lysipomia, and Lobelia section Tupa form a Pan-Andean radiation with broad habitat diversity. This clade is a prime candidate for investigations of Neotropical biogeography and morphological evolution.

A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

BACKGROUND

Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species.

RESULTS

The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3-28.8 Ma), and crown Bovidae (17.3-15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record.

CONCLUSIONS

The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how phylogeographic and paleoenvironmental hypotheses inferred from a tree containing only extant taxa can be problematic without consideration of the fossil record. Incorporating the fossil record of Ruminantia is a necessary step for future analyses aiming to reconstruct the evolutionary history of this clade.