New insights into the molecular phylogeny and taxonomy of mormyrids (Osteoglossiformes,Actinopterygii) in northern East Africa

Based on morphological data and analysis of mitochondrial cytochrome b gene and nuclear (S7 intron 1) DNA sequences, the phylogenetic relationships of all Pollimyrus species known from the Omo‐Turkana enclosed basin and Nile system below the Murchison Falls were solved. A mormyrid “Pollimyrus” petherici is distantly related to all other studied Pollimyrus species and clusters together with Cyphomyrus species forming with the later a monophyletic group. Moreover, the West African (but not the Congo River) populations of Cyphomyrus psittacus, the type species of the genus, seem to be conspecific to C. petherici. That is, the range of the genus Cyphomyrus is extended toward the Nile and Omo‐Turkana basins. This genus belongs to the large clade widely distributed in sub‐Saharian Africa and characterized by the presence of a chin appendage. Significance of this character for mormyrid phylogeny is discussed. Two distinct lineages of Pollimyrus occurring sympatrically in the White Nile tributaries and previously reported as the light and dark forms of Pollimyrus isidori together with five other congeneric species studied form a monophyletic group. The light form apparently represents P. isidori distributed in the Nile system downstream of the Murchison Falls and West Africa; the dark‐colored form (designated as Pollimyrus “D”) represents a distinct phylogenetic lineage inhabiting both the Omo‐Turkana and the White Nile basin. Morphological and ecological data suggest that this form may be conspecific to East African Pollimyrus nigricans or most probably represents a new species.     

The biogeography and phylogeny of schizothoracine fishes (Schizopygopsis) in the Qinghai‐Tibetan Plateau

Freshwater fish belonging to the genus Schizopygopsis are widespread in drainages throughout the Qinghai‐Tibetan Plateau and, thus, a model group with which to investigate how paleo‐drainage changes linked to historical uplifting within the Qinghai‐Tibetan Plateau influence speciation. To date, the phylogenetic and taxonomic relationships within Schizopygopsis remain controversial. In this study, we constructed a comprehensive molecular phylogeny of Schizopygopsis based on six mitochondrial gene sequences. We compared the taxonomic relationships revealed by this phylogeny with those obtained from morphological data. We also used this phylogeny to assess the extent to which the evolution of Schizopygopsis has been driven by paleo‐drainage changes linked to uplifting of the Qinghai‐Tibetan Plateau. Results indicated that all Schizopygopsis taxa formed a monophyletic group comprising five major clades, which were inconsistent with the taxonomic relationships based on morphology for this group. Our results also strongly supported the validity of S. anteroventris and S. microcephalus as distinct species within Schizopygopsis. Molecular calibrations showed that species within the middle Yangtze species diverged earlier (~4.5 Mya) than species within the Indus River (~3.0 Mya), the Mekong River (~2.8 Mya) and the Tsangpo + Salween rivers (~2.5 Mya). The most recent evolutionary splits occurred among species from the upper and lower Yangtze River, the Yellow River and the Qiadam Basin at about 1.8 to 0.3 Mya. Our molecular evidence and use of the molecular clock calibration have allowed us to associate speciation events within the genus Schizopygopsis to the formation and separation of paleo‐drainage connections caused by tectonic events during the uplifting of the Qinghai‐Tibetan Plateau (~4.5 Mya). This work underlines the dominant role of vicariance in shaping the evolutionary history of the genus Schizopygopsis. Further research using multiple loci and more extensive sampling will reveal a more complete picture of the phylogenetic relationships and biogeography of Schizopygopsis fishes.     

Phylogeny and species delimitation of North European Lumbricillus (Clitellata,Enchytraeidae)

The enchytraeid genus Lumbricillus comprises about 80 described species of clitellate worms, which are up to a few centimetres long, and they mostly inhabit the littoral zone of non‐tropical marine and brackish waters world‐wide. The phylogeny of this genus is poorly studied, but previous work has suggested that Lumbricillus is a non‐monophyletic group. In this study, species boundaries and the phylogeny of this genus is re‐assessed using more than 300 DNA‐barcoded specimens (using COI mtDNA), part of which was also sequenced for two additional mitochondrial and four nuclear molecular markers. Statistical and coalescent based applications were used for the delimitation of a total of 24 species, of which 20 were identified as belonging to 17 described morphospecies; one morphospecies was found to be a complex of four delimited species, and another four delimited species could not be matched with any described species. Furthermore, gene trees, concatenation and multispecies coalescent based species trees were estimated using Bayesian inference. The estimated phylogenies confirm a non‐monophyletic Lumbricillus as L. semifuscus is clearly excluded from the genus. Furthermore, the placement of a monophyletic clade consisting of L. arenarius, L. dubius, and an unidentified species varies between analyses; they are either found as the sister‐group to the genus Grania or as sister‐group to the remaining Lumbricillus, where the latter relationship is supported by the multispecies coalescent, which we consider as the most reliable method.     

Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia

Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid‐late Miocene significantly affected the diversification of the genus in these areas.     

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

Sponges are among the most species‐rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model‐based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single‐copy nuclear protein‐coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax, C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera, C. longissima, C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model‐based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.     

A multiple‐gene phylogeny reveals polyphyly among eastern North American Aphaenogaster species (Hymenoptera: Formicidae)

Twenty‐three Aphaenogaster species (Hymenoptera: Formicidae) occur in North America. While morphology and ecology define most species, the species limits of a group in the Eastern United States are unclear. In particular, the morphological and behavioural characters of A. carolinensis, A. picea and A. rudis overlap. These observations suggest that these three species are not monophyletic. We therefore tested the monophyly of Aphaenogaster in the context of molecular phylogenetic analyses. We used DNA data from five genes: CO1, CAD, EF1αF2, long‐wavelength rhodopsin and wingless, to reconstruct phylogenies for 44 Aphaenogaster and outgroup species. In the resulting trees, reconstructed using parsimony and Bayesian inference, species boundaries associated with well‐supported monophyletic clades of individuals in most of the 23 North American Aphaenogaster collected from multiple locations. However, some clades were unresolved, and both A. picea and A. rudis were not monophyletic. Although this may indicate that clades of multiple species represent fewer but morphologically varied species, given the short branch lengths, the lack of resolution may reflect the fact that these ants have recently radiated, and a lack of gene lineage sorting explains the non‐monophyly of species. Additional biological information concerning pre‐ and postmating barriers is needed before a complete revision of species boundaries for Aphaenogaster.     

Molecular evidence for species level divergence in African Nile Crocodiles Crocodylus niloticus (Laurenti, 1786)

Relationships of the newly discovered dwarf crocodiles from Mauritania were inferred from mitochondrial 12S sequences. Specimens from 13 different Crocodylus niloticus populations (from East Africa, West Africa and Madagascar) were compared. Additional representatives of the genus Crocodylus (one from Africa and one from Australia), the African genus Osteolaemus and the South American alligatorid Paleosuchus palpebrosus (as outgroup) were included in the analysis. Maximum-likelihood and Bayesian analyses yielded relationships that were strikingly different from currently prevailing phylogenetic hypotheses. Both analyses consistently revealed two groups, one consisting of the monophyletic West- and Central African populations and the other of a paraphyletic group containing the East African and Madagascan populations. High genetic divergence between those groups indicates separation on the species level. Furthermore ‘C’ cataphractus is clearly shown not to be a member of the genus Crocodylus. The resulting nomenclatural changes are discussed. To cite this article: A. Schmitz et al., C. R. Palevol 2 (2003).     

The origin and divergence of Gobioninae fishes (Teleostei: Cyprinidae) based on complete mitochondrial genome sequences

The gudgeons (subfamily Gobioninae) are a group of cyprinid fishes primarily distributed in East Asia. However, studies on their origins and divergence are scarce. Here the whole mitochondrial genome sequences of 27 gudgeon species (including one newly determined), 22 other cyprinid species, and two non‐cyprinids as outgroups are applied to infer the evolution of the gudgeons. Based on Bayesian and maximum likelihood phylogenetic analyses, the gudgeons were determined to be a monophyletic group which can be further subdivided into four monophyletic clades with strong supports. The divergence times of the gudgeons were estimated using a relaxed molecular clock method; the results indicate that these fishes originated in the early Paleocene (approx. 63.5 Mya) and that the basal Hemibarbus group diverged from the other gudgeon fishes (approx. 58.3 Mya). As an independent group the Coreius began to diverge from the remaining two groups (approx. 54.6 Mya); the most derived two groups diverged from each other (approx. 53.6 Mya). The divergences of the four gudgeon groups were within a relatively short time frame (approx. 58–53 Mya). Based on the reconstruction of evolutionary trends of gudgeon habitat, evidence is provided that supports the origin and differentiation of this fauna as being associated with some special paleo‐environmental events occurring from the early Paleocene to the Pliocene. The study represents comprehensive molecular dating and character evolution analyses of the gudgeons, and providing a valuable framework for future research in the evolution of the Gobioninae fishes.     

Geographical structure,narrow species ranges,and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts

The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL‐F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum‐likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9–93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2–52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio‐Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long‐distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large‐scale distribution of humid tropical angiosperm forests in the Eocene.     

A phylogenetic analysis of Pseudopaludicola (Anura) providing evidence of progressive chromosome reduction

Here, we present a molecular phylogenetic analysis of the Neotropical genus Pseudopaludicola focusing on species relationships including 11 of the 17 known species of Pseudopaludicola; several samples of Pseudopaludicola are not assigned to any species; and 34 terminal species as an outgroup. The study was based on the analysis of approximately 2.3 kb of the sequence of the mitochondrial 12S rRNA, tRNA^val and 16S rRNA genes through maximum parsimony and Bayesian phylogenetic reconstruction approaches. Our results showed that Pseudopaludicola is a well‐supported monophyletic group organized into four major clades and confirmed that the assemblage of species that lack T‐shaped terminal phalanges is paraphyletic with respect to the P. pusilla Group. Chromosomal data mapped on the cladogram showed a direct correlation among the four clades and observed chromosome numbers (2n = 22, 20, 18 and 16) with a progressive reduction in the chromosome number. Overall, our findings suggest that some taxonomic changes are necessary and reinforce the need for a revision of the genus Pseudopaludicola.     

Diversification of Lupinus (Leguminosae) in the western New World: derived evolution of perennial life history and colonization of montane habitats

Previous phylogenetic studies of Lupinus (Leguminosae) based on nuclear DNA have shown that the western New World taxa form a monophyletic group representing the majority of species in the genus, with evidence for high rates of recent diversification in South America following final uplift of the Andes 2–4 million years ago (Mya). For this study, three regions of rapidly evolving non-coding chloroplast DNA (trnL intron, trnS–trnG, and trnT–trnL) were examined to estimate the timing and rates of diversification in the western New World, and to infer ancestral states for geographic range, life history, and maximum elevation. The western New World species (5.0–9.3 Mya, 0.6–1.1 spp./My) comprise a basally branching assemblage of annual plants endemic to the lower elevations of western North America, from which two species-rich clades are recently derived: (i) the western North American perennials from the Rocky Mountains, Great Basin, and Pacific Slope (0.7–2.1 Mya, 2.0–5.9 spp./My) and (ii) the predominantly perennial species from the Andes Mountains of South America and highlands of Mexico (0.8–3.4 Mya, 1.4–5.7 spp./My). Bayesian posterior predictive tests for association between life history and maximum elevation demonstrate that perennials are positively correlated with higher elevations. These results are consistent with a series of one or more recent radiations in the western New World, and indicate that rapid diversification of Lupinus coincides with the derived evolution of perennial life history, colonization of montane habitats, and range expansion from North America to South America.     

Three New Freshwater Cochliopodium Species (Himatismenida,Amoebozoa) from the Southeastern United States

Cochliopodium is a lens‐shaped genus of Amoebozoa characterized by a flexible layer of microscopic dorsal scales. Recent taxonomic and molecular studies reported cryptic diversity in this group and suggested that the often‐used scale morphology is not a reliable character for species delineation in the genus. Here, we described three freshwater Cochliopodium spp. from the southeastern United States based on morphological, immunocytochemistry (ICC), and molecular data. A maximum‐likelihood phylogenetic analysis and pairwise comparison of COI sequences of Cochliopodium species showed that each of these monoclonal cultures were genetically distinct from each other and any described species with molecular data. Two of the new isolates, “crystal UK‐YT2” (Cochliopodium crystalli n. sp.) and “crystal‐like UK‐YT3” (C. jaguari n. sp.), formed a clade with C. larifeili, which all share a prominent microtubule organizing center (MTOC) and have cubical‐shaped crystals. The “Marrs Spring UK‐YT4” isolate, C. marrii n. sp., was 100% identical to “Cochliopodium sp. SG‐2014 KJ569724 .” These sequences formed a clade with C. actinophorum and C. arabianum. While the new isolates can be separated morphologically, most of the taxonomic features used in the group show plasticity; therefore, Cochliopodium species can only be reliably identified with the help of molecular data.     

Phylogenetic relationships among species of the Neotropical genus Graomys (Rodentia: Cricetidae): contrasting patterns of skull morphometric variation and genetic divergence

Subtle differences of external traits characterize species of rodents in the Neotropical genus Graomys. On the other hand, the species differ markedly in chromosome number. In the present study, we evaluate the possible evolutionary forces involved in the evolution of the genus by assessing the degree of intra‐ and interspecific genetic and morphological variation. A phylogenetic analysis demonstrates the existence of at least three species with high levels of genetic distance (10%), which diverged between 1 and 1.5 Mya. Neither Graomys griseoflavus, nor Graomys chacoensis present marked phylogeographical structure. Regarding morphological characters, these species show shape differences in the skull that could be attributable to differences in the local conditions they inhabit, being more marked in G. griseoflavus than in G. chacoensis. The skull shape of G. chacoensis could have evolved under genetic drift, whereas evidence reported in the present study indicates that this character could be under selective pressures in G. griseoflavus. Reconstruction of the ancestral area suggests that G. griseoflavus originated in the central Monte desert, whereas G. chacoensis originated in the Chaco ecoregion surrounding the austral extreme of the Yungas rainforest. Subsequently, both species would have undergone demographic and geographical expansions almost simultaneously, starting approximately 150 000–175 000 years ago. The complex evolutionary history of the genus could be partly explained by the decoupling of morphological, karyological and molecular traits.     

Phylogenetics,delimitation and historical biogeography of the pantropical tree genus Thespesia (Malvaceae,Gossypieae)

Thespesia consists of 16 species of trees and shrubs from Southeast Asia–Oceania, Africa and America, the most well known being T. populnea, a small tree of tropical coastal areas around the world. Phylogenetic relationships in the genus and among its allies in tribe Gossypieae were inferred using three plastid and two nuclear regions to ascertain its generic delimitation and explore its biogeographical history. Maximum‐likelihood and Bayesian analyses confirmed that Thespesia is not monophyletic and, based on these results, Azanza is reinstated to accommodate the two species previously placed in Thespesia section Lampas. Dating analyses and ancestral range estimation indicated that Thespesia s.s. most likely originated in Southeast Asia–Oceania c. 30 Mya, but extant species did not begin to differentiate until the late Miocene. Two dispersal events, one into Africa c. 11 Mya and another into America (Antilles) c. 9 Mya, gave rise to the African and the Greater Antillean endemics, respectively. The two most widespread hydrochorous species, T. populnea and T. populneoides, originated in Southeast Asia–Oceania from where they spread to other parts of the world. Our analysis also indicated a much earlier origin than previously reported for the eumalvoid clade and its tribes Gossypieae, Malveae and Hibisceae suggesting that vicariance might have had an important role early in the history of these groups.     

A new type of 3‐D peripheral ultrastructure in Glaucocystis (Glaucocystales,Glaucophyta) as revealed by ultra‐high voltage electron microscopy

The coccoid glaucophyte genus Glaucocystis is characterized by having a thick cell wall, which has to date prohibited examination of the native ultrastructural features of the protoplast periphery. Recently, however, the three‐dimensional (3‐D) ultrastructure of the protoplast periphery was revealed in two divergent Glaucocystis species, with the world's most powerful ultra‐high voltage electron microscope (UHVEM). The two species exhibit morphological diversity in terms of their 3‐D ultrastructural features. However, these two types do not seem to encompass actual ultrastructural diversity in the genetically diverse genus Glaucocystis. Here, we report a new type of peripheral 3‐D ultrastructure resolved in “G. incrassata” SAG 229‐2 cells by 3‐D modeling based on UHVEM tomography using high‐pressure freezing and freeze‐substitution fixation. The plasma membrane and underlying flattened vesicles in “G. incrassata” SAG 229‐2 exhibited grooves at intervals of 200–600 nm, and the flattened vesicles often overlapped one another at the protoplast periphery. This 3‐D ultrastructure differs from those of the two types previously reported in other species of Glaucocystis. The possibility of classification of Glaucocystis species based on the 3‐D ultrastructure of the protoplast periphery is discussed.     

Species‐level phylogeographical history of the endemic species Calligonum roborovskii and its close relatives in Calligonum section Medusa (Polygonaceae) in arid north‐western China

Quaternary climatic oscillations appear to have influenced the genetic diversity and evolutionary history of arid‐adapted plants. To understand the processes involved and reveal evolutionary relationships, haplotypes were examined from Calligonum roborovskii, an endemic species occurring in the arid zones across the desert regions of north‐western China, and seven other species also from Calligonum section Medusa, including C. gobicum, C. mongolicum and the narrow endemic species C. ebi‐nuricum, C. pumilum, C. taklimakanense, C. trifarium and C. yengisaricum. Forty‐three haplotypes were identified in 422 individuals from 51 natural populations, from variation of two plastid DNA intergenic spacers (rpl32‐trnL and ycf6‐psbM). A high level of total genetic diversity was found across species for which more than two populations were examined, including C. gobicum, C. mongolicum, C. pumilum and C. roborovskii. A distinct isolation‐by‐distance pattern in each of these species was suggested by the Mantel test, indicating that restricted gene flow caused high genetic differentiation among populations. Three haplotypes were shared by two or three species each, but the other 40 haplotypes were species‐specific. The 43 haplotypes split into three major clades, but not species‐specific lineages; most of the Calligonum species were not reciprocally monophyletic, probably due to incomplete lineage sorting or introgression. The identified haplotypes were dated to 1.97 Mya (95% highest posterior density: 2.95–0.99 Mya) and diverged until the late Pleistocene, possibly linked to aridification and enlargement of deserts caused by climate changes. Variation of desert habitats during the Pleistocene might play a key role in causing the divergence.     

Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers,continuous characters and geometric morphometric data

The monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.     

Molecular phylogeny of the marine littoral genus Cafius (Coleoptera: Staphylinidae: Staphylininae) and implications for classification

Jeon, M.‐J., Song, J.‐H. & Ahn, K.‐J. (2012). Molecular phylogeny of the marine littoral genus Cafius (Coleoptera: Staphylinidae: Staphylininae) and implications for classification. —Zoologica Scripta, 41, 150–159. A phylogenetic analysis of the marine littoral genus Cafius Stephens is presented based on molecular characters. The data set comprised partial mitochondrial COI (910 bp), COII (369 bp), 12S rDNA (351–354 bp), 16S rDNA (505–509 bp) and nearly complete sequences of 18S rDNA (1814–1830 bp) for 37 species. Twenty‐seven Cafius species, representing five of six subgenera, two Remus Holme species, three Phucobius Sharp species, monotypic Thinocafius Steel and four outgroups were included. The sequences were analysed simultaneously by parsimony analysis in Tree Analysis Using New Technology (TNT) with traditional manual alignment, direct optimization (DO) in the program POY4 under a variety of gap costs and partitioned Bayesian analysis for the combined data. The genus Cafius and nearly all of its subgenera were not supported as being monophyletic. Instead, all analyses (parsimony trees, DO tree under equal weighting and Bayesian tree) showed monophyly of Cafius + Phucobius + Remus + Thinocafius (clade Z) and all seven nested clades (A–G). However, the phylogenetic relationships among clades A–G differed among the analyses. The genus Phucobius was recovered as a monophyletic group within Cafius. The genus Remus was not monophyletic but formed a clade with C. rufescens Sharp and C. rufifrons Bierig within Cafius. The genus Thinocafius formed a clade with C. caviceps Broun, C. litoreus (Broun) and C. quadriimpressus (White) within Cafius. We propose new concepts for the genus Cafius and its related genera, and the seven nested clades.