HYBRIDS AND PHYLOGENETIC SYSTEMATICS I. PATTERNS OF CHARACTER EXPRESSION IN HYBRIDS AND THEIR IMPLICATIONS FOR CLADISTIC ANALYSIS

Interspecific hybridization is considered common among plants, but the methods of cladistic systematics produce only divergently branching phylogenetic hypotheses and thus cannot give the correct phylogeny if an analysis includes hybrids. Empirical studies of the impact of known hybrids on phylogenetic analysis are lacking, and are necessary to begin to understand the problems that we face if hybrids are often included in cladistic analysis. Examination of the implications of hybrids for cladistics must begin with patterns of character expression in hybrids. This study includes 17 hybrids and their nine parental taxa that are Central American species of Aphelandra (Acanthaceae), analyzed using a set of 50 morphological characters. The hybrids are overwhelmingly intermediate as quantitatively scored for phylogenetic analysis. They express maternal and paternal, and primitive and derived characters in equal frequencies, showing no evidence of predominant inheritance of derived character states as has been assumed by most cladists who have considered hybrids theoretically. Because of their known genetic constitution, hybrids were useful in homology assessment and ordering character states. The parental character set was generally robust, but some changes were made to reflect the special evidence offered by the hybrids. These hybrids suggest that the inclusion of hybrids in phylogenetic analysis will not lead to unresolved cladograms with rampant homoplasy, as has been predicted by other authors. Instead, the patterns of character inheritance in these hybrids lead to the prediction that a hybrid will be placed by phylogenetic analysis as a basal lineage to the clade that includes its most derived parent, with relatively little effect on homoplasy. These predictions will be evaluated by incorporation of the hybrids in phylogenetic analyses, to be reported in a subsequent paper.     

A reexamination of infraspecific taxa of a wild potato,Solanum microdontum (Solanum sect.Petota:Solanaceae)

Current taxonomic interpretations ofSolanum microdontum Bitter partition the species into two or three infraspecific taxa, variously recognized as subspecies or varieties. The present study reexamines these taxa using morphological data from four individuals each of 69 accessions from most of the range of the species, planted in a common field plot. Our results show that the character states used to recognize infraspecific taxa inS. microdontum often vary within accessions and have no correlation with geography. We conclude that past hypotheses have used typological concepts and that infraspecific taxa are not warranted. This study questions other hypotheses of infraspecific taxa in sect.Petota.     

Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships

The relationships among basal sauropodomorphs are controversial. Results of cladistic analyses vary from a fully paraphyletic assemblage to a monophyletic core‐prosauropod. We apply the comparative cladistics method to three published cladistic analyses of sauropodomorph dinosaurs, in order to identify root causes for differences between phylogenetic results. Except for three taxa (Saturnalia, Thecodontosaurus, and Efraasia) and one clade (Gravisauria), the remaining genera are recovered with conflicting positions. The comparative method is based on indices that allow for the quantification of the degree of similarity in characters and character states among analyses. A comparison of primary data, character selection, and scoring highlights significant discrepancies in data sets. Our results suggest that one character out of two varies from one analysis to the other. These are the root causes for the phylogenetic incongruence observed. The hurdle of the phylogenetic definition of the clade Sauropoda, which has been defined in four different ways, is also treated. We concur with several recent papers following the first node‐based definition of Sauropoda. © 2015 The Linnean Society of London     

Reproductive variance in planar spawning Chromodoris species (Mollusca: Nudibranchia)

Although variance in life history parameters is well known from comparisons among broad phylogenetic groups of marine invertebrates, there is still an outstanding need to increase empirical studies that compare closely related species. If the species under study share a recent common ancestor and developmental strategy, there is an opportunity to contrast maternal investment against interspecific variation while controlling for evolutionary distance. Furthermore, when these species co-occur, it allows for exploration of potential character displacement. We examined egg size and other factors related to reproduction in four closely related species, co-occurring nudibranchs belonging to the monophyletic Chromodoris planar spawning clade. The duration of oviposition appeared to be conserved and may be phylogenetically constrained in these four co-occurring species. In contrast, egg size differed significantly among species, but was not influenced by parental body length or position within the egg mass for any of the species. The number of egg mass whorls also varied, but did not correspond to the interspecific differences in parental body length. These results suggest that some significant differences exist among these sympatric Chromodoris species that may be candidate traits for character displacement. These characters would need to be re-measured in geographic areas where the studied Chromodoris species do not co-occur.     

Phylogenetic analysis of the Amphitritinae (Polycnaeta: Terebellidae)

The phylogenetic relationships of the Amphitritinae (Polychaeta: Terebellidae) were studied using parsimony analysis of 22 external morphological characters. To choose outgroups to polarize the characters, I carried out a preliminary analysis of the relationships of the four terebellid subfamilies and the Trichobranchidae. The single most parsimonious tree from the analysis supports monophyly of the Terebellidae by the presence of ventral glandular shields. However, this character is homoplasious within the Terebellomorpha, and further evaluation of the Terebellidae is recommended. Artacama and Thelepus were chosen as outgroups for the analysis of amphitritine genera. The generic level analysis yielded seven equally parsimonious trees, which are consistent in their topologies except for the relationships among seven genera in one large clade. In all trees, Artacama is the sister taxon to a large clade within the Amphitritinae; the Artacaminae is therefore synonymized with the Amphitritinae, which is diagnosed by the presence of double rows of uncini. Within the Amphitritinae, the status of several monotypic genera is questioned; plesiomorphic character states indicated by the analysis are discussed. The results presented are offered as working hypotheses of the relationships among amphitritine genera. The large number of homoplasies indicated by the analysis emphasizes the need to further evaluate these hypotheses using additional characters. With a robust phylogenetic hypothesis of amphitritine relationships, a re-classification of the group based on apomorphic character states can be undertaken, and questions regarding the evolution of morphological characters, reproductive modes, or biogeographical patterns can be properly addressed.     

Leaf epidermal character variation and evolution in Gaultherieae (Ericaceae)

The taxonomic value and evolutionary significance of 30 leaf epidermal characters from 238 samples representing 127 species of all seven genera in the tribe Gaultherieae (Ericaceae) and two outgroup genera were investigated by scanning electron microscopy. The character states were coded and optimized onto a maximum‐likelihood tree based on previous molecular data with Fitch parsimony and hierarchical Bayesian analysis to trace the evolution of character states throughout all internodes in the phylogenetic tree for Gaultherieae. Leaf epidermal characters were found to be largely consistent within species, but highly variable at interspecific and higher taxonomic levels. The most recent common ancestral states of 15 characters diagnosed various lineages recovered from prior studies, some with no prior morphological support. Relatively high frequencies of state change occur in the eastern Asian clade Gaultheria series Gymnobotrys + Diplycosia, the American clade G. subsection Dasyphyta p.p., the core East Asian clade and the Australia/New Zealand clade. The characters with the highest frequencies of state change are the outer stomatal ledge ornamentation type, the stomatal apparatus level, stomatal density and area, and the type of abaxial trichomes. These character state change patterns may provide insight into the ecological adaptions of Gaultherieae during their evolutionary history. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 686–710.     

Phylogenetics of global Camellia (Theaceae) based on three nuclear regions and its implications for systematics and evolutionary history

Camellia contains tea, oil camellia, and camellias which benefit people globally. Its infrageneric classification is, however, controversial and unstable, and former phylogenetic analyses failed to yield robust and consistent trees. Here, we aimed to reconstruct a robust phylogenetic tree, date all clades and discuss the evolutionary history of Camellia. Emphasizing the taxonomically comprehensive sampling rather than more DNA data, orthologous nuclear RPB2 introns 11–15 and 23, and waxy were sequenced for 99 taxa of Camellia to reconstruct its phylogenetic history. Ten clades are identified in Camellia: Camellia II, Camelliopsis, Corallina, Furfuracea, Heterogenea, Paracamellia, Piquetia, Stereocarpus, Thea and Yellow camellias II. Camellia grijsii and C. shensiensis are not closely related with other oil camellias that form the clade Paracamellia. Sections Camelliopsis and Theopsis together form the clade Camelliopsis, while clade Furfuracea consists of sect. Furfuracea and C. hongkongensis. Camellia connata is separated from C. lanceolata but nested in the clade Heterogenea, and C. longissima is nested in the clade Thea, suggesting a new germplasm for tea breeding. Molecular dating using four fossil calibration points suggests that the crown age of Camellia is 39.5 Ma with clade Corallina probably the earliest infrageneric clade to diversify and the most widespread clade, Paracamellia, the latest. Our findings provide new insights into the phylogenetic relationships, systematics and evolutionary history of Camellia.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Revised classification of the Cyanidiophyceae based on plastid genome data with descriptions of the Cavernulicolales ord. nov. and Galdieriales ord. nov. (Rhodophyta)

The Cyanidiophyceae, an extremophilic red algal class, is distributed worldwide in extreme environments. Species grow either in acidic hot environments or in dim light conditions (e.g., “cave Cyanidium”). The taxonomy and classification systems are currently based on morphological, eco-physiological, and molecular phylogenetic characters; however, previous phylogenetic results showed hidden diversity of the Cyanidiophyceae and suggested a revision of the classification system. To clarify phylogenetic relationships within this red algal class, we employ a phylogenomic approach based on 15 plastomes (10 new) and 15 mitogenomes (seven new). Our phylogenies show consistent relationships among four lineages (Galdieria, “cave Cyanidium”, Cyanidium, and Cyanidioschyzon lineages). Each lineage is distinguished by organellar genome characteristics. The “cave Cyanidium” lineage is a distinct clade that diverged after the Galdieria clade but within a larger monophyletic clade that included the Cyanidium and Cyanidioschyzon lineages. Because the “cave Cyanidium” lineage is a mesophilic lineage that differs substantially from the other three thermoacidophilic lineages, we describe it as a new order (Cavernulicolales). Based on this evidence, we reclassified the Cyanidiophyceae into four orders: Cyanidiales, Cyanidioschyzonales, Cavernulicolales ord. nov., and Galdieriales ord. nov. The genetic distance among these four orders is comparable to, or greater than, the distances found between other red algal orders and subclasses. Three new genera (Cavernulicola, Gronococcus, Sciadococcus), five new species (Galdieria javensis, Galdieria phlegrea, Galdieria yellowstonensis, Gronococcus sybilensis, Sciadococcus taiwanensis), and a new nomenclatural combination (Cavernulicola chilensis) are proposed.     

Phylogeny of subsect. Meleuphorbia (A. Berger) Pax & Hoffm. (Euphorbia L.) reflects the climatic regime in South Africa

The nuclear ITS region and four noncoding cpDNA regions were directly sequenced to reconstruct the phylogeny of subsect. Meleuphorbia (Euphorbia L.), which is endemic to South Africa. Sequence polymorphism within cpDNA regions was too low to permit phylogenetic analyses. Large deletions including the ctp2-atpB proximal promoter in the atpB-rbcL IGS were found in two individuals. Phylogeny of subsect. Meleuphorbia was reconstructed using nrITS sequence data. The two resulting major clades are consistent with the geographic distribution of the investigated taxa. Plants distributed in the winter rainfall area in the Little Karoo form one clade, plants growing in the Great Karoo with predominant summer rainfall form the other. Subsect. Meleuphorbia is not monophyletic, because members of subsect. Anthacantha are clustered within the meleuphorbias. Both share functional unisexuality, form angled stems and the key character of Anthacantha (inflorescence spines) occurs as a transitional stage in form of persistent peduncles in Meleuphorbia.     

A molecular phylogenetic study of Cucujidae s.l. (Coleoptera: Cucujoidea)

Of all the superfamilies within the megadiverse order Coleoptera (Insecta), Cucujoidea (Cucujiformia) is arguably the most problematic taxonomically. The families comprising Cucujidae s.l. (Silvanidae, Laemophloeidae, Passandridae and Cucujidae s.s. represent a large portion of cucujoid diversity. Herein we present the results of a rigorous molecular phylogenetic analysis of Cucujidae s.l. using maximum‐likelihood and Bayesian analyses of seven genes. Representatives of over half of the families of Cucujoidea (excluding the cerylonid series), as well as a broad sampling of Silvanidae and Laemophloeidae, were analysed. The monophyly of Cucujidae s.l. is rejected but a subgrouping of taxa that may form the core of a natural cucujoid lineage is recovered. This clade consists of two large monophyletic groups including several families each. Relationships among these smaller cucujoid groups are discussed, including several novel phylogenetic hypotheses, whereas morphological characters considered significant for classification in Cucujidae s.l. are evaluated in light of these phylogenetic hypotheses. Silvaninae, Telephanini, Brontini and Brontinae are recovered as monophyletic in the Bayesian analysis, but the former two are recovered as paraphyletic in the maximum‐likelihood analysis. Our results support the placement of Psammoecus Latreille within Telephanini and also recover a paraphyletic Telephanus Erichson. Silvaninae is divided into three lineages, each representing a potential tribal lineage. Laemophloeidae is rendered paraphyletic in all analyses by Propalticidae and the latter is herein formally transferred to Laemophloeidae stat.n . Several suprageneric laemophloeid clades are recovered and discussed as potential higher‐level groups. Laemophloeus Dejean is not recovered as monophyletic.     

Mainland colonization by island lizards

Aim We investigate biogeographic relationships within the lizard genus Anolis Daudin, 1802 to test the hypothesis that the mainland (Central and South American) Norops‐clade species descended from a West Indian Anolis ancestor. Previous hypotheses have suggested that close island relatives of mainland Norops species (the Cuban Anolis sagrei and Jamaican A. grahami series) represent over‐water dispersal from a mainland ancestor. These previous hypotheses predict that the A. sagrei and A. grahami series should be phylogenetically nested within a Norops clade whose ancestral geography traces to the mainland. If Norops is West Indian in origin, then West Indian species should span the deepest phylogenetic divergences within the Norops clade. Location Central and South America and West Indian islands. Methods The phylogenetic relationships of Anolis lizards are reconstructed from aligned DNA sequences using both parsimony and Bayesian approaches. Hypotheses are tested in two ways: (1) by reconstructing the ancestral geographic location for the Norops clade using Pagel & Lutzoni's (2002) Bayesian approach, and (2) by testing alternative topological arrangements via Wilcoxon Signed‐Ranks tests ( Templeton, 1983 ) and Shimodaira–Hasegawa tests ( Shimodaira & Hasegawa, 1999 ). Results Our evidence supports an origin of mainland Norops anoles from a West Indian ancestor. A West Indian ancestor to the Norops clade is statistically supported, and alternatives to the biogeographic pattern [Cuban (Jamaican, Mainland)] are statistically rejected by Shimodaira–Hasegawa tests, although not by Wilcoxon Signed‐Ranks tests. Main conclusions Our data support the hypothesis of a West Indian origin for mainland Norops. This result contradicts previous hypotheses and suggests that island forms may be an important source for mainland biodiversity.     

Multilocus phylogeny of the widely distributed South American lizard clade Eulaemus (Liolaemini,Liolaemus)

The lizard genus Liolaemus and different clades within it have been the focus of several recent phylogenetic studies mainly based on morphology and mtDNA. Although there is general consensus for recognizing two clades (subgenera) within the genus, [Liolaemus (sensu stricto) and Eulaemus], phylogenetic relationships within each subgenus remain difficult to elucidate, given incomplete taxonomic sampling and large discordance between published studies. Here, new phylogenetic relationships for the Eulaemus subgenus are proposed based on the largest molecular data set ever used for this clade, which includes 188 individuals and 14 loci representing different parts of the genome (mtDNA, anonymous nuclear loci and nuclear protein‐coding loci). This data set was analysed using two species tree approaches (*beast and MDC). Levels of discordance among methods were found, and with previously published studies, but results are robust enough to propose new phylogenetic hypotheses for the Eulaemus clade. Specifically well‐resolved and well‐supported novel hypotheses are provided within the lineomaculatus section, and we formally recognize the zullyae clade, the sarmientoi clade and the hatcheri group. We also resolve species relationships within the montanus section, and particularly within the melanops series. We found discordance between mitochondrial and nuclear trees and discussed alternative hypotheses for the lineomaculatus and montanus sections, as well as the challenge in resolving phylogenetic relationships for large clades in general.     

MOLECULAR PHYLOGENETIC ANALYSIS OF LIFE-HISTORY EVOLUTION IN ASTERINID STARFISH

We analyzed phylogenetic relationships among 12 nominal species of starfish in the genera Patiriella and Asterina (Order Valvatida, Family Asterinidae), based on complete sequences for a mitochondrial protein coding gene (cytochrome oxidase subunit I) and five mitochondrial transfer RNA genes (alanine, leucine, asparagine, glutamine, and proline) (1923 bp total). The resulting phylogeny was used to test a series of hypotheses about the evolution of life-history traits. (1) A complex, feeding, planktonic larva is probably ancestral for these starfish, but this is not the most parsimonious reconstruction of ancestral larval states. (2) The feeding larval form was lost at least four times among these species, and three of these losses occurred among members of a single clade. (3) Small adult size evolved before both cases of hermaphroditism and viviparous brooding, but viviparity was not always preceded by an intermediate form of external brooding. (4) An ordered transformation series from feeding planktonic development to viviparous brooding has been predicted for starfish, but we could not find an example of this transformation series. (5) Viviparity evolved recently (< 2 Mya). (6) Both species selection and transformation of lineages may have contributed to the accumulation of species with nonfeeding development among these starfish. (7) Neither Asterina nor Patiriella are monophyletic genera. Larval forms and life-history traits of these starfish have evolved freely under no obvious constraints, contrary to the widely assumed evolutionary conservatism of early development.     

The atlas–axis complex in Dibamidae (Reptilia: Squamata) and their potential relatives: The effect of a fossorial lifestyle on the morphology of this skeletal bridge

We report on the first detailed study of the atlas–axis complex in the lizard clade Dibamidae, a family of poorly known fossorial squamates distributed in tropical or subtropical climates. This skeletal bridge is characterized by several features, such as the complete absence of the first intercentrum or the appearance of the first free cervical rib on the axis (usually less developed in Dibamus relative to that in Anelytropsis). Our study shows morphological differences of the atlas–axis complex in the Mexican blind lizard Anelytropsis relative to those of Asian Dibamus, the only two known extant genera of this clade. With regard to taxonomy and phylogenetic topology of the Dibamidae within Squamata, a huge conflict exists between morphology versus molecules. The morphology of the atlas–axis complex is therefore compared with several potential sister clades + Sphenodon. Dibamids share several features with limbless Gekkota, Scincoidea, and Amphisbaenia. The complete absence of the first intercentrum is observed in Rhineura floridana and in Ateuchosaurus chinensis as well, and the free rib associated with the synapophyses of the axis is also present in Acontias meleagris. However, some of these features may result from a limbless, burrowing ecology and thus could represent homoplastic characters. In any case, the morphology of the atlas–axis shows that dibamids share most character states with skinks. Although the atlas–axis complex forms only an additional source of information, this conclusion is consistent with most morphological rather than molecular tree topologies.     

Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the β-fibrinogen gene in avian molecular systematics

The common raven (Corvus corax) is one of the most widely distributed and recognizable avian species in the world. Recent molecular work, however, described two mitochondrial lineages of the common raven, termed the Holarctic clade and the California clade, and questioned the monophyly of this taxon by placing the Chihuahuan raven (C. cryptoleucus) sister to the California clade. We evaluated this phylogenetic hypothesis with additional sequence data and increased taxon sampling. We used ～3.7 kb of DNA sequence data from sections of the mitochondrial coding genes COI, cyt b and ND4, a fragment of the non‐coding mitochondrial DNA control region, and the entire intron 7 of the nuclear β‐fibrinogen gene (β‐fibint 7). We combined these DNA sequence data to erect hypotheses of relationships for lineages of the common raven and related taxa. Maximum parsimony, maximum likelihood, and Bayesian methods yield a paraphyletic common raven. These analyses nest the Chihuahuan raven within the common raven, with strong support for a sister relationship between the Chihuahuan raven and the California clade. In addition, the pied crow (C. albus) is also nested within the common raven, and is sister to the Holarctic clade. Our analyses reveal the challenge of determining phylogenetic relationships and species boundaries in this morphologically conservative genus, and suggest that future molecular work with increased taxon sampling will uncover cryptic species and novel evolutionary relationships. Lastly, this survey is one of a growing number of avian phylogenetic studies to employ either β‐fibint 7 or COI, and the first to use ND4. We developed a simple procedure for comparing rates of evolution in molecular markers, and show that in Corvus the nuclear intron β‐fibint 7 is evolving at a considerably slower pace than the mitochondrial markers, while COI is evolving at a slower rate than cyt b, and ND4 approximately the same rate as cyt b. Hence, β‐fibint 7 and other individual nuclear introns may have limited utility in resolving relationships among recently evolved taxa, whereas both COI and ND4 should be useful in a wide range of avian molecular genetic investigations.     

Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re‐examined traditional characters used to define species groups and used multivariate statistics to quantitatively evaluate group structure in morphometric space. Clustering analyses of phenotypic similarity indicate that some (but not all) members of previously defined species groups are phenotypically most similar to other members of the same group. However, when species group membership was mapped on our partitioned Bayesian phylogenetic hypothesis, only one species group corresponds to a clade; all other species group arrangements are strongly rejected by our phylogeny. Our results demonstrate that (1) previously recognized species group relationships were misled by phenotypic convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple lineages have independently invaded the Philippines. Based on this new perspective on the phylogenetic relationships of Philippine Sphenomorphus, we revise the archipelago's diverse assemblage of species at the generic level, and resurrect and/or expand four previously recognized genera, and describe two new genera to accommodate the diversity of Philippine skinks of the Sphenomorphus group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1217–1243.     

The molecular phylogenetics of Trachymyrmex Forel ants and their fungal cultivars provide insights into the origin and coevolutionary history of ‘higher‐attine’ ant agriculture

The fungus‐growing ants and their fungal cultivars constitute a classic example of a mutualism that has led to complex coevolutionary dynamics spanning c. 55–65 Ma. Of the five agricultural systems practised by fungus‐growing ants, higher‐attine agriculture, of which leaf‐cutter agriculture is a derived subset, remains poorly understood despite its relevance to ecosystem function and human agriculture across the Neotropics and parts of North America. Among the ants practising higher‐attine agriculture, the genus Trachymyrmex Forel, as currently defined, shares most‐recent common ancestors with both the leaf‐cutter ants and the higher‐attine genera Sericomyrmex Mayr and Xerolitor Sosa‐Calvo et al. Although previous molecular‐phylogenetic studies have suggested that Trachymyrmex is a paraphyletic grade, until now insufficient taxon sampling has prevented a full investigation of the evolutionary history of this group and limited the possibility of resolving its taxonomy. Here we describe the results of phylogenetic analyses of 38 Trachymyrmex species, including 27 of the 49 described species and at least 11 new species, using four nuclear markers, as well as phylogenetic analyses of the fungi cultivated by 23 species of Trachymyrmex using two markers. We generated new genetic data for 112 ants (402 new gene sequences) and 95 fungi (153 new gene sequences). Our results corroborate previous findings that Trachymyrmex, as currently defined, is paraphyletic. We propose recognizing two new genera, Mycetomoellerius gen.n. and Paratrachymyrmex gen.n. , and restricting the continued use of Trachymyrmex to the clade of nine largely North American species that contains the type species [Trachymyrmex septentrionalis (McCook)] and that is the sister group of the leaf‐cutting ants. Our fungal cultivar phylogeny generally corroborates previously observed broad patterns of ant–fungus association, but it also reveals further violations of those patterns. Higher‐attine fungi are divided into two groups: (i) the single species Leucoagaricus gongylophorus (Möller); and (ii) its sister clade, consisting of multiple species, recently referred to as Leucoagaricus Singer ‘clade B’. Our phylogeny indicates that, although most non‐leaf‐cutting higher‐attine ants typically cultivate species in clade B, some species cultivate L. gongylophorus, whereas still others cultivate fungi typically associated with lower‐attine agriculture. This indicates that the attine agricultural systems, which are currently defined by associations between ants and fungi, are not entirely congruent with ant and fungal phylogenies. They may, however, be correlated with as yet poorly understood biological traits of the ants and/or of their microbiomes.