Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences

The coding region of the matK gene was sequenced to infer the phylogeny of the family Magnoliaceae. Phylogenetic analyses of 21 matK sequences representing ten genera of Magnoliaceae and three outgroups suggest relationships among both subfamilies and genera. Monophyly of the subfamily Liriodendroideae (the genus Liriodendron) and the subfamily Magnolioideae is strongly supported, respectively. Within the subfamily Magnolioideae, three clades are formed: (1) the genus Magnlietia, (2) the subgenus Magnolia, and (3) the subgenus Yulania, with the genera Michelia, Paramichelia, Tsoongiodendron, Alcimandra, Kmeria, Parakmeria and Manglietiastrum. However, the genus Magnolia is shown to be a polyphyletic group, and the genus Michelia a paraphyletic group. Relatively low sequence divergences are detected among genera of the the subfamily Magnolioideae, ranging from 0.14% to 1.70%, especially in the tribe Micheliinae (0.14–0.98%). Molecular evidence from matK sequence data suggests that the phylogenetic positions and the delimitation of the eight genera Magnolia, Michelia, Tsoongiodendron, Paramichelia, Alcimandra, Kmeria, Parakmeria and Manglietiastrum need to be reconsidered. Received: 2 January 2000 / Accepted: 12 February 2000     

The phylogeny of the BEP clade in grasses revisited: evidence from the whole-genome sequences of chloroplasts

Despite the considerable efforts to reconstruct the phylogeny of grasses, the relationships among the subfamilies Bambusoideae, Pooideae and Ehrhartoideae in the BEP clade remain unresolved. Here we completely sequenced three chloroplast genomes of representative species from Bambusoideae and Ehrhartoideae and obtained 19 additional chloroplast genome sequences of other grasses from GenBank. Using sequences of 76 chloroplast protein-coding genes from the 22 grass species, we fully resolved the phylogeny of the BEP clade. Our results strongly supported the (B,P)E hypothesis, i.e., Bambusoideae and Pooideae are more closely related than Ehrhartoideae. This result was not biased by systematic or sampling errors and was impervious to phylogenetic methods or model specification. The divergence time estimate suggests that the initial diversification of the BEP clade into three subfamilies happened within a short time period (≈ 4 MY). The presence of these short internal branches may explain the inability of previous studies to achieve a confident resolution of the BEP clade. The combination of the sequences of the entire chloroplast genomes provided sufficient phylogenetic information to resolve the BEP phylogeny fully. These results provide a valuable evolutionary framework for comparative and functional genomic studies using the grass family as a model system.     

Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera: Hesperioidea)

A comprehensive tribal‐level classification for the world’s subfamilies of Hesperiidae, the skipper butterflies, is proposed for the first time. Phylogenetic relationships between tribes and subfamilies are inferred using DNA sequence data from three gene regions (cytochrome oxidase subunit I‐subunit II, elongation factor‐1α and wingless). Monophyly of the family is strongly supported, as are some of the traditionally recognized subfamilies, with the following relationships: (Coeliadinae + (“Pyrginae” + (Heteropterinae + (Trapezitinae + Hesperiinae)))). The subfamily Pyrginae of contemporary authors was recovered as a paraphyletic grade of taxa. The formerly recognized subfamily Pyrrhopyginae, although monophyletic, is downgraded to a tribe of the “Pyrginae”. The former subfamily Megathyminae is an infra‐tribal group of the Hesperiinae. The Australian endemic Euschemon rafflesia is a hesperiid, possibly related to “Pyrginae” (Eudamini). Most of the traditionally recognized groups and subgroups of genera currently employed to partition the subfamilies of the Hesperiidae are not monophyletic. We recognize eight pyrgine and six hesperiine tribes, including the new tribe Moncini. © The Willi Hennig Society 2008.     

High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae)

Background

Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies.

Methodology/Principal Findings

Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae.

Conclusions/Significance

The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly.     

Using molecules and morphology to infer the phylogenetic relationships and evolutionary history of the Dirini (Nymphalidae: Satyrinae), a tribe of butterflies endemic to Southern Africa

The first empirically supported phylogenetic hypothesis of relationships for the southern African endemic butterfly tribe Dirini is presented. Data derived from the morphology and ecology of the adults and immature stages (33 characters), and portions of the mitochondrial gene cytochrome oxidase I (COI) and the nuclear genes elongation factor 1α (EF1α) and wingless (WG) (totalling 1734 bp) were used to infer the relationships of the in‐group genera. An expanded molecular dataset using four genera from the Nymphalini and Satyrini to root the tree, and three genera from the Melanitini to test the monophyly of the tribe, was analysed using parsimony and Bayesian methods. Estimates of divergence times were calculated using two fossil calibrations under a relaxed molecular clock model. The monophyly of the tribe and each in‐group genus were strongly supported. Key findings are the sister‐taxon relationship of Aeropetes and Tarsocera, the apparent simultaneous or nearly simultaneous radiation of four lineages, the polyphyly of the species within Torynesis, and the apparent trans‐Atlantic dispersal of the ancestors of Manataria about 40 Ma. Estimates of divergence times indicate that the tribe has undergone two major radiations since its origin: the first when they left forest habitats in the mid–late Oligocene, shortly after the radiation of the grasses (Poaceae), and the second in the early‐middle Pliocene, coinciding with the aridification of southern Africa and the spread of conditions that favoured C₄ grasses over the C₃ grasses that dirine larvae prefer to eat. The high species diversity within the tribe appears to be partly a taxonomic artefact that may have resulted from the misinterpretation of climate‐related phenotypic variation within extant species. Relocation and breeding experiments should test this hypothesis.     

Astragalus (Fabaceae): A molecular phylogenetic perspective

Nucleotide sequences of the plastidmatK gene and nuclear rDNA internal transcribed spacer region were sampled fromAstragalus L. (Fabaceae), and its closest relatives within tribe Galegeae, to infer phylogenetic relationships and estimate ages of diversification. Consistent with previous studies that emphasized sampling for nrDNA ITS primarily within either New World or Old World species groups,Astragalus, with the exception of a few morphologically distinct species, is strongly supported as monophyletic based on maximum parsimony and Bayesian analyses ofmatK sequences as well as a combined sequence dataset. ThematK data provides better resolution and stronger clade support for relationships amongAstragalus and traditionally related genera than nrDNA ITS.Astragalus sensu stricto plus the genusOxytropis are strongly supported as sister to a clade composed of strictly Old World (African, Australasian) genera such asColutea. Sutherlandia, Lessertia, Swainsona, andCarmichaelia, plus several morphologically distinct segregates of EurasianAstragalus. Ages of these clades and rates of nucleotide substitution estimated from a fossil-constrained, rate-smoothed, Bayesian analysis ofmatK sequences sampled from Hologalegina indicateAstragalus diverged from its sister group,Oxtropis, 12–16 Ma, with divergence of Neo-Astragalus beginning ca 4.4. Ma. Estimates of absolute rates of nucleotide substitution forAstragalus and sister groups, which range from 8.9 to 10.2×10⁻¹⁰ substitutions per site per year, are not unusual when compared to those estimated for other, mainly temperate groups of papilionoid legumes. The results of previously published work and other recent developments on the phylogenetic relationships and diversification ofAstragalus are reviewed.     

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

The taxonomy of Bambusoideae is in a state of flux and phylogenetic studies are required to help resolve systematic issues. Over 60 taxa, representing all subtribes of Bambuseae and related non-bambusoid grasses were sampled. A combined analysis of five plastid DNA regions, trnL intron, trnL-F intergenic spacer, atpB-rbcL intergenic spacer, rps16 intron, and matK, was used to study the phylogenetic relationships among the bamboos in general and the woody bamboos in particular. Within the BEP clade (Bambusoideae s.s., Ehrhartoideae, Pooideae), Pooideae were resolved as sister to Bambusoideae s.s. Tribe Bambuseae, the woody bamboos, as currently recognized were not monophyletic because Olyreae, the herbaceous bamboos, were sister to tropical Bambuseae. Temperate Bambuseae were sister to the group consisting of tropical Bambuseae and Olyreae. Thus, the temperate Bambuseae would be better treated as their own tribe Arundinarieae than as a subgroup of Bambuseae. Within the tropical Bambuseae, neotropical Bambuseae were sister to the palaeotropical and Austral Bambuseae. In addition, Melocanninae were found to be sister to the remaining palaeotropical and Austral Bambuseae. We discuss phylogenetic and morphological patterns of diversification and interpret them in a biogeographic context.     

Cladistic analysis of morphological characters in the eulophine tribe Cirrospilini (Hymenoptera: Eulophidae)

A total of 56 morphological characters were analyzed for 53 cirrospiline species that represent all of the 17 described genera of the tribe. The other taxa of the Eulophinae included in the analysis were six species of six representative genera in the tribe Eulophini, a species of Elasmus (the only genus comprising the tribe Elasmini), and a species of Trichospilus (unplaced). Trichospilus and two of the six genera of Eulophini examined were placed within Cirrospilini. Monophyly of Cirrospilini (when these two genera of Eulophini and Trichospilus are included) and of the cirrospiline genera for which more than one species were examined was supported, but the relationships between the genera were poorly resolved. An exception was Cirrospilus, the largest genus in the Cirrospilini, monophyly of which was not supported to any extent.     

Duthieeae,a new tribe of grasses (Poaceae) identified among the early diverging lineages of subfamily Pooideae: molecular phylogenetics,morphological delineation,cytogenetics and biogeography

The phylogeny of Pooideae, one of the largest subfamilies of grasses, has been intensively studied during the past years. To investigate the early evolutionary splits in Pooideae we used a broad sample of genera with uncertain placement, some of which have not been studied in molecular phylogenetics before, complemented by representatives from other lineages of this subfamily. Morphological, cytogenetic and biogeographical analyses were added to the molecular sequence work on chloroplast matK–3’trnK and nuclear ITS. According to chloroplast DNA data, a new and well-supported lineage was identified among the early branches. It consisted of Phaenosperma and a larger group of genera encompassing Anisopogon, Danthoniastrum, Duthiea, Metcalfia, Pseudodanthonia (inclusion resting on ITS and morphology), Sinochasea and Stephanachne. Based on structural characters we suggest to keep Phaenosperma under the monotypic tribe Phaenospermateae and to accommodate the other genera under a new tribe Duthieeae, which is morphologically well-defined by synapomorphic spikelet features. Megalachne and Podophorus were not part of the early diverging Pooideae lineages but belong to the Aveneae/Poeae complex. Morphological characteristics of Duthieeae are discussed with respect especially to Stipeae and reveal consistent differences between both tribes. The genera of Duthieeae and the major lineages of Stipeae are keyed. A cytogenetic survey of exemplary taxa corroborates high chromosome base numbers as prevailing within the early diverging lineages of Pooideae, but chromosome sizes are more highly varied than previously reported. Ecogeographical analyses point to warm and humid conditions as the ancestral bioclimatic niche of Phaenosperma and Duthieeae, whereas adaptation to cold and drought occurred only in a part of Duthieeae but was obviously less successful than in the widespread and much more species-rich tribe Stipeae. The distribution of Duthieeae with species-poor or monotypic genera in mountains of the northern hemisphere and Anisopogon as an outlier in Australia suggests relict character.     

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.     

EVOLUTIONARY ANALYSIS OF THE LARGE SUBUNIT OF CARBOXYLASE (rbcL) NUCLEOTIDE SEQUENCE AMONG THE GRASSES (GRAMINEAE)

The full nucleotide sequences of the chloroplast encoded large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) are available for nine grass species and partial sequence data for one species. Relative rate tests of the “molecular clock” hypothesis suggest that rbcL evolved more rapidly in the lineage leading to Zea than in those leading to the other species. The estimated overall substitution rate for rbcL among these grasses is about 5 times 10^?10 substitutions per site per year, or about one-half the synonymous rate. The nine full sequences were analyzed by the UPGMA, Wagner parsimony, maximum likelihood, and Fitch-Margoliash methods. The latter three methods produced trees with the same topology. This topology largely agrees with current taxonomic evidence regarding the relationships among these grasses. UPGMA produced a topology that conflicts more substantially with available taxonomic evidence. Statistical comparison of the three alternative topologies for the subfamilies Panicoideae, Pooideae and Bambusoideae failed to support one of these topologies over the others, reflecting the taxonomic ambiguities surrounding the relationships among these taxa. Phylogenetic analyses based on the partial sequences of all 10 species gave conflicting results with regard to the relationship between Hordeum and Triticum, both members of the tribe Triticeae. This indicates that rbcL sequences contain too little information to resolve relationships among genera within this tribe. Overall, the results suggest that rbcL sequence data can provide some new information concerning grass phylogeny, but that the amount of available data from this gene is too small to differentiate statistically among alternative topologies for the grasses. Conflicting results from parsimony, maximum likelihood, and Fitch-Margoliash methods proved useful in exploring the validity of assumptions underlying these methods.     

Pollen morphology of the Pavetteae (Rubiaceae,Ixoroideae) and its taxonomic significance

Pollen grains of the tribe Pavetteae (Rubiaceae, subfamily Ixoroideae) are examined using LM and SEM. Grains are 3‐ or 4‐colporate and (semi‐) tectate (in one Versteegia species atectate). Sexine patterns vary between perforate, microreticulate, reticulate, rugulate and striato‐reticulate. Supratectal elements are sometimes present. The variation in pollen morphology in the Pavetteae allows to recognize seven pollen types, the distribution of which is useful to evaluate generic delimitations and relationships within the tribe. Pollen characters corroborate the close relationships between the genera Coleactina, Dictyandra and Leptactina and between Homollea, Homolliella and Paracephaelis. All the genera of the tribe proved to be stenopalynous (the species examined possess the same pollen type), except Pavetta, Rutidea, Versteegia and Tarenna which are eurypalynous. In the huge genus Pavetta the existing infrageneric classification is supported pollen morphologically. Pollen morphology further indicates that the genus Tarenna is badly delimited and strongly in need of a revision. The small genus Versteegia is in need of further taxonomic and palynological study to understand the pollen morphological variation encountered here. At a higher rank, pollen morphology also does not contradict the recent division of the Pavetteae in the Ixoreae (a stenopalynous tribe with presumably primitive pollen) and the Pavetteae sensu stricto (eurypalynous).     

Phylogeny of the tribe Aveneae (Pooideae, Poaceae) inferred from plastid trnT-F and nuclear ITS sequences

New insights into evolutionary trends in the economically important oat tribe (Aveneae) are presented. Plastid trnT-F and nuclear ribosomal ITS sequences were used to reconstruct the phylogeny of the Aveneae-Poeae-Seslerieae complex (Pooideae, Poaceae) through Bayesian- and maximum parsimony-based analyses, separately and in combination. The plastid data identified a strongly supported core Aveneae lineage that separated from other former Aveneae and Poeae groups. Koeleriinae, Aveninae, and Agrostidinae emerged as the main groups of this core Aveneae, which also included other minor subgroups with uncertain relationships and a few former Poeae members. Several former Aveneae representatives were also placed in independent sublineages in Poeae. Seslerieae resolved as close allies of Poeae or Aveneae in the plastid and nuclear topologies, respectively. Because of the intermingling of some Aveneae and Seslerieae lineages in Poeae and vice versa, we propose to expand Poeae to include all the aforementioned lineages. This best reflects our current understanding of the phylogeny of these important temperate grasses and sheds light on their evolutionary history.     

Phylogeny of the plant bug subfamily Mirinae (Hemiptera: Heteroptera: Cimicomorpha: Miridae) based on total evidence analysis

The first comprehensive phylogenetic analyses of the most diverse subfamily of plant bugs, Mirinae, is presented in this study, for 110 representative taxa based on total evidence analysis. A total of 85 morphological characters and 3898 bp of mitochondrial (16S, COI) and nuclear (18S, 28S) sequences were analysed for each partitioned and combined dataset based on parsimony, maximum likelihood and Bayesian inference. Major results obtained in this study include monophyly of the tribe Mecistoscelini. The largest tribe, Mirini, was recovered as polyphyletic, and Stenodemini was recovered as paraphyletic. The clade of Stenodemini + Mecistoscelini is the sister group of the remaining Mirinae. The monophyly of two complexes composed of superficially similar genera were tested; the Lygus complex was recovered as nonmonophyletic, and the Adelphocoris–Creontiades–Megacoelum complex was confirmed to be monophyletic. The generic relationships of the main clades within each tribe based on the phylogeny, as well as their supported morphological characters, are discussed.     

Molecular phylogeny of the grass genus Brachypodium P. Beauv. based on RFLP and RAPD analysis

Nuclear genome analysis using RFLPs and RAPDs has been assessed within different species of the genus Brachypodium P. Beauv. and representatives of other grasses in order to determine the characteristics of the Brachypodium genome and to establish its evolutionary position in relation to other Pooideae. Distinctive features of the Brachypodium genome are its small size, the low amount of repetitive DNA, the lack of restriction fragment length polymorphisms within the genus for the assayed probe/enzyme combinations, and the genomic variability demonstrated at species level by random DNA amplification. These molecular studies confirm Brachypodium as an isolated ancient genus best placed in its own tribe (Brachypodieae). Its relationships to other tribes Bromeae, Triticeae, Poeae are resolved, Brachypodieae being the earliest tribe to diverge from this core of pooids. Within the genus two major Old World clades are distinguishable: an annual clade, represented only by B. distachyon; and a perennial clade, represented by all the other species studied (except B. mexicanum). The perennial American species B. mexicanum appears equally attached to these two clades. RFLP data were found to be useful in obtaining phylogenies at generic and higher rank levels, whereas the highly variable RAPD data were more suitable for resolving interspecific and intraspecific evolutionary pathways.     

Phylogenetic relationships of Combretoideae (Combretaceae) inferred from plastid,nuclear gene and spacer sequences

Phylogenetic relationships of the subfamily Combretoideae (Combretaceae) were studied based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) regions, the plastid rbcL gene and the intergenic spacer between the psaA and ycf3 genes (PY-IGS), including 16 species of eight genera within two traditional tribes of Combretoideae, and two species of the subfamily Strephonematoideae of Combretaceae as outgroups. Phylogenetic trees based on the three data sets (ITS, rbcL, and PY-IGS) were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Partition-homogeneity tests indicated that the three data sets and the combined data set are homogeneous. In the combined phylogenetic trees, all ingroup taxa are divided into two main clades, which correspond to the two tribes Laguncularieae and Combreteae. In the Laguncularieae clade, two mangrove genera, Lumnitzera and Laguncularia, are shown to be sister taxa. In the tribe Combreteae, two major clades can be classified: one includes three genera Quisqualis, Combretum and Calycopteris, within which the monophyly of the tribe Combreteae sensu Engler and Diels including Quisqualis and Combretum is strongly supported, and this monophyly is then sister to the monotypic genus Calycopteris; another major clade includes three genera Anogeissus, Terminalia and Conocarpus. There is no support for the monophyly of Terminalia as it forms a polytomy with Anogeissus. This clade is sister to Conocarpus. Electronic Publication     

Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data

DNA sequence data from the chloroplast noncoding rpl16 intron are used to address phylogenetic relationships among the major lineages of the grass family, with particular emphasis on the highly heterogeneous subfamily Bambusoideae and the basal lineages. Thirty-five grass sequences representing all six currently recognized major groups of the family and one outgroup sequence were analyzed using both parsimony and distance methods. The phylogenetic analyses indicated: (1) Puelia, a traditionally isolated bambusoid genus, is the most basal lineage in the BOP clade (Bambusoideae, Oryzoideae, and Pooideae); (2) the bambusoid clade is a sister group to the pooid clade; and (3) the monophyletic oryzoid clade is well separated from the bambusoid clade. The study further confirmed the recognition of two primary groups in the grass family: the BOP clade and the PACC clade (Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae); it also provided further evidence that the traditional subfamily Bambusoideae is highly heterogeneous and phylogenetically unacceptable. The data support Streptochaeteae, Anomochloeae, and Phareae as the most basal lineages among the extant grasses. Within the BOP clade, oryzoids and pooids are confirmed as two monophyletic clades, but the bambusoid clade, including only the woody bamboo tribe Bambuseae and the herbaceous bamboo tribe Olyreae, is relatively weakly supported. The study also indicated that the chloroplast noncoding region sequence data could be useful in phylogenetic analysis at relatively high taxonomic levels.     

Relationships within the Munnopsidae (Crustacea, Isopoda, Asellota) based on three genes

The Munnopsidae are a diverse group of asellote isopods that are an important component of deep‐sea fauna. Morphologically‐based phylogenetic inference attempts have proven to be of limited use due to the ecological and morphological diversity within the clade. Monophyly of the family is well‐established but relationships within the group remain unresolved. This project is the first molecularly‐based effort focused specifically on resolving phylogenetic relationships within the Munnopsidae. Partial 28S and COI and complete 18S genes were sequenced for 28 asellotes, 15 additional taxa were included from which only one or two of the three target sequences could be obtained, and 18S sequences for five additional taxa were available from GenBank. Sequences were analysed both as individual genes and in combination using Bayesian and maximum parsimony approaches. Each gene provided a phylogenetic signal that could be identified in the combined analyses, with 18S analyses providing the most resolution of phylogenetic relationships. The available representatives of subfamilies Munnopsinae and Ilyarachninae were monophyletic, as was the genus Munneurycope. Relationships within the subfamily Munnopsinae were well‐resolved by thorough taxon sampling, several new species were placed, and the need for taxonomic revision of Munnopsis/Munnopsoides was supported. These analyses supported putative Eurycope paraphyly and emphasized the need for careful revision of this highly variable genus. Tytthocope was sister to Munnopsurus. Syneurycope was suggested as the sister group to the ilyarachnines. Combined analyses provided increased support for clades suggested in at least two individual gene analyses and for clades not strongly contradicted by individual analyses. Further work is required to fully resolve the munnopsid phylogeny and should consist of increased taxon sampling for the complete 18S sequence and possibly identification of at least one slowly evolving, nuclear protein‐coding gene to resolve the basal polytomy and enable placement of the root.     

The diversification of South American murid rodents: evidence from mitochondrial DNA sequence data for the akodontine tribe

Phylogenetic relationships based on 801 base pairs (bp) of the mitochondrial cytochrome b gene are examined for eight genera and 28 species of the akodontine tribe of South American murid rodents. The akodontine tribe comprises some 35% of the total diversity of the subfamily Sigmodontinae, but the current taxonomy at virtually all levels is uncertain because of inadequate generic diagnoses and assessments of variation and trends in traditional morphological characters. Monophyly of the tribe cannot be resolved by the sequence data, based on comparisons to outgroup taxa in three other tribes (Oryzomyini, Phyllotini, and Thomasomyini). However, highly corroborated monophyletic units within the group are obtained in a variety of both parsimony and distance analyses. These include a redefined and numerically dominant genus Akodon (with Microxus and Hypsimys as synonyms), Bolomys, Lenoxus, Oxymycterus, and a strongly supported assemblage that includes the central Andean Chroeomys and 'Akodon' andinus and the southern Abrothrix, 'Akodon' olivaceus, and the long-clawed mice of the genera Notiomys, Geoxus, and Chelemys. Sequence divergence within species is typically less than 5%, although levels can reach 10% for some highly polytypic forms. Divergence among genera within the tribe reaches 35% in corrected estimates, a level that is as great as that among representatives of different tribes. Changes in the current classification of akodontines are suggested based on these data, and the timing and place of origin of the tribe and its radiation is discussed.