Phylogenetic synthesis of morphological and molecular data reveals new insights into the higher‐level classification of Tipuloidea (Diptera)

Tipuloidea, the crane flies, are a diverse lineage of true flies (Insecta: Diptera) whose phylogenetic classification and taxonomy remain a challenge. Here we present the results of a quantitative phylogenetic analysis of Tipuloidea based on combined morphological characters (adult, larvae and pupae) and nuclear gene sequence data (28S rDNA and CAD). Forty‐five species, from 44 genera and subgenera, were sampled, representing the four putative families of Tipuloidea (Cylindrotomidae, Limoniidae, Pediciidae and Tipulidae sensu stricto). Analyses of individual datasets, although differing in overall topology, support the monophyly of several major lineages within Tipuloidea. Parsimony and Bayesian analyses using individual morphological and molecular datasets resulted in incongruent topologies. Increased resolution and tree support was obtained when both datasets (morphology and genes) were combined, in both combined evidence parsimony and Bayesian analyses, than when analysed separately. The recovered consensus phylogeny was not consistent with any previously proposed Tipuloidea classification, with previous importance assigned to character states shown here to represent losses and reversals seen as a major factor influencing erroneous classification. The results provided here, together with evidence from previous analyses, were used to append the Tipuloidea classification to supported evolutionary lineages. Tipuloidea is presented as two families: Pediciidae and Tipulidae. Pediciidae is recovered as the sister group to all remaining Tipuloidea. Our current phylogenetic hypothesis is not consistent with the existing subfamilial classification of the ‘Limoniidae’, which is paraphyletic with respect to a well‐supported Tipulinae + Cylindrotominae clade, whereas the three ‘limoniid’ subfamilies are para‐ or polyphyletic. The recognition of ‘Limoniidae’ as a valid monophyletic family is discouraged and the subfamilies of ‘Limoniidae’ are amended and placed within Tipulidae. A revised phylogenetic classification is proposed for the crane flies based on a synthesis of evidence from multiple genes and morphology.     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships

Evolutionary developmental biology ("evo-devo") has revolutionized evolutionary biology but has had relatively little impact on systematics. We show that similar large-scale developmental changes in distantly related lineages can dramatically mislead phylogenetic analyses based on morphological data. Salamanders are important model systems in many fields of biology and are of special interest in that many species are paedomorphic and thus never complete metamorphosis. A recent study of higher-level salamander phylogeny placed most paedomorphic families in a single clade based on morphological data. Here, we use new molecular and morphological data to show that this result most likely was caused by the misleading effects of paedomorphosis. We also provide a well-supported estimate of higher-level salamander relationships based on combined molecular and morphological data. Many authors have suggested that paedomorphosis may be problematic in studies of salamander phylogeny, but this hypothesis has never been tested with a rigorous phylogenetic analysis. We find that the misleading effects of paedomorphosis on phylogenetic analysis go beyond the sharing of homoplastic larval traits by paedomorphic adults, and the problem therefore is not solved by simply excluding suspected paedomorphic characters. Instead, two additional factors are critically important in causing paedomorphic species to be phylogenetically "misplaced": (1) the absence of clade-specific synapomorphies that develop during metamorphosis in nonpaedomorphic taxa and allow their "correct" placement and (2) parallel adaptive changes associated with the aquatic habitat of the larval stage. Our results suggest that the effects of paedomorphosis on phylogenetic analyses may be complex, difficult to detect, and can lead to results that are both wrong and statistically well supported by parsimony and Bayesian analyses.     

Systematics of naviculoid diatoms (Bacillariophyta): A preliminary analysis of protoplast and frustule characters for family and order level classification

The relationships between 49 naviculoid diatoms, currently arranged in 14 families and four orders were investigated using cladistic analysis in order to test the types of characters used in diatom systematics and to assess how well the current classification reflects possible phylogenetic relationships in this group. Some of the families and orders comprise taxa with different protoplast characters, or taxa with similar protoplast arrangements are placed in separate families or orders. Therefore as both cell wall and protoplast characters were used, three analyses were undertaken; total data, protoplast data and frustule data. The analyses support the recognition of the Mastogloiales (unequivocally) and the Cymbellales (largely) but indicate that some of the familial groupings are more ambiguous. The members of the Berkeleyaceae, Berkeleya, Parlibellus and Climaconeis, were never grouped together and Achnanthes brevipes never grouped with the other monoraphid diatoms, but usually with members of the Mastogloiales (total and protoplast data). Similarly, Round et al.’s familial groupings within the Cymbellales do not emerge from our analyses. Our results support the hypothesis that monoraphid genera have arisen independently from different naviculoid diatoms, and that Achnanthes sensu stricto should be transferred to the Mastogloiales. Some of the problems associated with incomplete information and inaccurate terminology are discussed briefly.     

The natural variation of a neural code

The way information is represented by sequences of action potentials of spiking neurons is determined by the input each neuron receives, but also by its biophysics, and the specifics of the circuit in which it is embedded. Even the "code" of identified neurons can vary considerably from individual to individual. Here we compared the neural codes of the identified H1 neuron in the visual systems of two families of flies, blow flies and flesh flies, and explored the effect of the sensory environment that the flies were exposed to during development on the H1 code. We found that the two families differed considerably in the temporal structure of the code, its content and energetic efficiency, as well as the temporal delay of neural response. The differences in the environmental conditions during the flies' development had no significant effect. Our results may thus reflect an instance of a family-specific design of the neural code. They may also suggest that individual variability in information processing by this specific neuron, in terms of both form and content, is regulated genetically.     

Restriction data from chloroplast DNA for phylogenetic reconstruction: Is there only one accurate way of scoring?

Information from the same restriction analysis of chloroplast DNA of 33 taxa ofRubiaceae was scored in four different ways, two of which were based on fragments, and two on restriction sites, and they were subsequently analysed with Wagner parsimony. The methods resulted in different phylogenetic trees. The inherent differences between the methods relate to the amount of non-homologous characters and dependent characters, but none of the methods will systematically bias the resulting cladograms. The fragment analyses are much less time-consuming, but probably less accurate, than the site analyses. The choice of method is dependent on a trade-off between accuracy and resources (time). One important recommendation is made: all phylogenetic analyses of chloroplast DNA data should be accompanied by a data matrix and contain information on how the matrix was compiled.     

Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.     

Phylogenetic inferences from molecular sequences: review and critique

Conflicting results often accompany phylogenetic analyses of RNA, DNA, or protein sequences across diverse species. Causes contributing to these conflicts relate to ambiguities in identifying homologous characters of alignments, sensitivity of tree-making methods to unequal evolutionary rates, biases in species sampling, unrecognized paralogy, functional differentiation, loss of phylogenetic informational content due to long branches or fast evolution, and difficulties with the assumptions and approximations used to infer phylogenetic relationships. Attempts to surmount these conflicts by averaging over many proteins are problematic due to inherent biases of selected families, lack of signal in others, and events of lateral transfer, fusion, and/or chimerism. The process of assessing reliability of the results using the bootstrap method is strewn with obstacles because of lack of independence and inhomogeneity in the molecular data. Problems inherent to the three major procedures for developing phylogenetic trees--parsimony, likelihood, distance--are reviewed. Special attention is given to the problem of inferring evolutionary distances from patterns of similarity among sequences. The difficulties encountered by methods of phylogenetic reconstructions based on the analysis of divergent sequence families make new methods based on the analysis of complete genomes reasonable alternatives. Several of these are considered, including the signature sequences of Gupta and associates, the study of genome profiles, and the genomic signature set forth by Karlin and colleagues.     

Morphological Evidence for the Phylogeny of Cetacea

A cladistic analysis of 54 extant and extinct cetacean taxa scored for 304 morphological characters supports a monophyletic Odontoceti, Mysticeti, Autoceta, and Cetacea. Forcing a sister-group relationship between Mysticeti and Physeteridae, as suggested by some, but not all, molecular studies, requires an additional 72 steps. In agreement with recent molecular studies, morphological data divide extant mysticetes into two clades: Balaenopteroidea (Eschrichtiidae + Balaenopteridae) and Balaenoidea (Balaenidae + Neobalaenidae). Cetotheriopsinae is removed from Cetotheriidae, elevated to Family Cetotheriopsidae, and placed within the Superfamily Eomysticetoidea. All extant mysticetes and all cetotheriids are placed in a new Parvorder Balaenomorpha, which is diagnosed by many morphological characters, including fusion of the anterior and posterior processes of petrosal to ectotympanic bulla, pronounced median keel on palate, and absence of ventral margin of sigmoid process of bulla. Many of the clades within Odontoceti in the most parsimonious trees of this study are at odds with recent phylogenetic analyses. For example, Platanistidae is not closely related to the extinct odontocete families Squalodontidae and Squalodelphinidae. Instead, it is more closely related to extant river-dwelling odontocetes (i.e., Lipotes, Inia), suggesting a single dispersal of odontocetes into freshwater habitats. We found several characters to support Physeteroidea (Physeteridae + Ziphiidae), a taxon considered paraphyletic by several molecular and some morphological analyses. Lack of agreement on the phylogeny within Odontoceti indicates that additional analyses, which include molecular and anatomical data as well as extant and extinct taxa, are needed.     

Phylogeny of Syrphidae (Diptera) inferred from combined analysis of molecular and morphological characters

Abstract.  Syrphidae (Diptera) commonly called hoverflies, includes more than 5000 species world-wide. The aim of this study was to address the systematic position of the disputed elements in the intrafamilial classification of Syrphidae, namely the monophyly of Eristalinae and the placement of Microdontini and Pipizini, as well as the position of particular genera ( Nausigaster , Alipumilio , Spheginobaccha ). Sequence data from nuclear 28S rRNA and mitochondrial COI genes in conjunction with larval and adult morphological characters of fifty-one syrphid taxa were analysed using optimization alignment to explore phylogenetic relationships among included taxa. A species of Platypezidae, Agathomyia unicolor , was used as outgroup, and also including one representative ( Jassidophaga villosa ) of the sister-group of Syrphidae, Pipunculidae. Sensitivity of the data was assessed under six different parameter values. A stability tree summarized the results. Microdontini, including Spheginobaccha , was placed basally, and Pipizini appeared as the sister-group to subfamily Syrphinae. The monophyly of subfamily Eristalinae was supported. The results support at least two independent origins of entomophagy in syrphids, and frequent shifts between larval feeding habitats within the saprophagous eristalines.     

Molecular insights into Cumacean family relationships (Crustacea, Cumacea)

Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many "diagnostic" characters are homoplasious.     

PHYLOGENETIC ANALYSES OF THE BRYOPSIDALES (ULVOPHYCEAE,CHLOROPHYTA) BASED ON RUBISCO LARGE SUBUNIT GENE SEQUENCES1

Current taxonomy of the Bryopsidales recognizes eight families; most of which are further categorized into two suborders, the Bryopsidineae and Halimedineae. This concept was supported by early molecular phylogenetic analyses based on rRNA sequence data, but subsequent cladistic analyses of morphological characters inferred monophyly in only the Halimedineae. These conflicting results prompted the current analysis of 32 taxa from this diverse group of green algae based on plastid‐encoded RUBISCO large subunit (rbcL) gene sequences. Results of these analyses suggested that the Halimedineae and Bryopsidineae are distinct monophyletic lineages. The families Bryopsidaceae, Caulerpaceae, Codiaceae, Derbesiaceae, and Halimediaceae were inferred as monophyletic, however the Udoteaceae was inferred as non‐monophyletic. The phylogenetic position of two taxa with uncertain subordinal affinity, Dichotomosiphon tuberosus Lawson and Pseudocodium floridanum Dawes & Mathieson, were also inferred. Pseudocodium was consistently placed within the halimedinean clade suggesting its inclusion into this suborder, however familial affinity was not resolved. D. tuberosus was the inferred sister taxon of the Halimedineae based on analyses of rbcL sequence data and thus a possible member of this suborder.     

MicroSyn: A user friendly tool for detection of microsynteny in a gene family

Background  

The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.     

A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data

DNA sequence data from plastid matK and trnL-F regions were used in phylogenetic analyses of Diurideae, which indicate that Diurideae are not monophyletic as currently delimited. However, if Chloraeinae and Pterostylidinae are excluded from Diurideae, the remaining subtribes form a well-supported, monophyletic group that is sister to a "spiranthid" clade. Chloraea, Gavilea, and Megastylis pro parte (Chloraeinae) are all placed among the spiranthid orchids and form a grade with Pterostylis leading to a monophyletic Cranichideae. Codonorchis, previously included among Chloraeinae, is sister to Orchideae. Within the more narrowly delimited Diurideae two major lineages are apparent. One includes Diuridinae, Cryptostylidinae, Thelymitrinae, and an expanded Drakaeinae; the other includes Caladeniinae s.s., Prasophyllinae, and Acianthinae. The achlorophyllous subtribe Rhizanthellinae is a member of Diurideae, but its placement is otherwise uncertain. The sequence-based trees indicate that some morphological characters used in previous classifications, such as subterranean storage organs, anther position, growth habit, fungal symbionts, and pollination syndromes have more complex evolutionary histories than previously hypothesized. Treatments based upon these characters have produced conflicting classifications, and molecular data offer a tool for reevaluating these phylogenetic hypotheses.     

Phylogenetic relationships and taxonomic ranking of pipizine flower flies (Diptera: Syrphidae) with implications for the evolution of aphidophagy

The taxonomic rank and phylogenetic relationships of the pipizine flower flies (Diptera: Syrphidae: Pipizini) were estimated based on DNA sequence data from three gene regions (COI, 28S and 18S) and 111 adult morphological characters. Pipizini has been treated as a member of the subfamily Eristalinae based on diagnostic adult morphological characteristics, while the larval feeding mode and morphology is shared with members of the subfamily Syrphinae. We analysed each dataset, both separately and combined, in a total evidence approach under maximum parsimony and maximum likelihood. To evaluate the influence of different alignment strategies of rDNA 28S and 18S genes on the resulting topologies, we compared the topologies inferred from a multiple alignment using fast Fourier transform (MAFFT) program with those topologies resulting from aligning the secondary structure of these rDNA genes. Total evidence analyses resolved pipizines as a sister group of the subfamily Syrphinae. Although the structural alignment and the MAFFT alignment differed in the inferred relationships of some clades and taxa, there was congruence in the placement of pipizines. The homogeneous morphology of the Pipizini clade in combination with their unique combination of characters among the Syrphidae suggest a change of rank to subfamily. Thus, we propose to divide Syrphidae into four subfamilies, including the subfamily Pipizinae stat. rev.     

Testing for divergent transmission histories among cultural characters: a study using Bayesian phylogenetic methods and Iranian tribal textile data

Background

Archaeologists and anthropologists have long recognized that different cultural complexes may have distinct descent histories, but they have lacked analytical techniques capable of easily identifying such incongruence. Here, we show how Bayesian phylogenetic analysis can be used to identify incongruent cultural histories. We employ the approach to investigate Iranian tribal textile traditions.

Methods

We used Bayes factor comparisons in a phylogenetic framework to test two models of cultural evolution: the hierarchically integrated system hypothesis and the multiple coherent units hypothesis. In the hierarchically integrated system hypothesis, a core tradition of characters evolves through descent with modification and characters peripheral to the core are exchanged among contemporaneous populations. In the multiple coherent units hypothesis, a core tradition does not exist. Rather, there are several cultural units consisting of sets of characters that have different histories of descent.

Results

For the Iranian textiles, the Bayesian phylogenetic analyses supported the multiple coherent units hypothesis over the hierarchically integrated system hypothesis. Our analyses suggest that pile-weave designs represent a distinct cultural unit that has a different phylogenetic history compared to other textile characters.

Conclusions

The results from the Iranian textiles are consistent with the available ethnographic evidence, which suggests that the commercial rug market has influenced pile-rug designs but not the techniques or designs incorporated in the other textiles produced by the tribes. We anticipate that Bayesian phylogenetic tests for inferring cultural units will be of great value for researchers interested in studying the evolution of cultural traits including language, behavior, and material culture.     

Phylogeny of Palaearctic Syrphidae (Diptera): evidence from larval stages

We estimated the phylogeny of Palaearctic Syrphidae using 187 larval morphological characters obtained from about 65% of the fauna (85 supraspecific taxa represented by 118 species) and based the analysis at the generic, level. The root of the syrphid tree was established from an outgroup consisting of other Aschizan families: the Platypezidae, Phoridae and Pipunculidae, with the tree rooted on the Lonchopteridae. The Syrphidae was the most derived Aschizan family. The Pipunculidae was the sister group to the Syrphidae. Eumerus was basal within Syrphidae. A trend exists towards increasing complexity of integumental folds and grooves across the Aschiza. In movement, the integument collapses along the line of these grooves. Grooves are evidence of muscles forming functional groups. Elaboration of independent groups of muscles appears to underlie much of the evolution of larval form within Aschiza. The basal feeding modes of syrphid larvae are mycophagy and phytophagy. Above these feeding modes, all remaining syiphids fall into one of two lineages comprising entomophages and saprophages, each of which has a single origin within the apparently polyphyletic Volucella. Major morphological innovation is associated with shifts between feeding modes; within feeding modes, change is gradual and tends towards increasing complexity. Change is mostly in structures associated with the mouthparts, thorax, anal segment and locomotory organs. Generic diagnoses with biological and taxonomic notes and a key to genera using larval characters are provided.     

Phylogenetic relationships of the genus Cheilosia and the tribe Rhingiini (Diptera, Syrphidae) based on morphological and molecular characters

The phylogenetic relationships of the tribe Rhingiini and the genus Cheilosia (Diptera, Syrphidae) were investigated using morphological and molecular characters. The genus Cheilosia is one of the most diverse lineages of hoverflies (Syrphidae). The mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), and the D2‐3 region of the nuclear 28S rRNA gene were chosen for sequencing, and morphological characters were scored for both adults and immature stages. The combined dataset included 56 ingroup taxa. The datasets were analyzed separately and in conjunction, using both static and dynamic alignment under the parsimony criterion. The aim of the study was to assess the phylogenetic relationships of the tribe Rhingiini, and to explore if the subgenera of Cheilosia were supported as monophyletic clades. Results showed that the monophyly of subtribes of Rhingiini remained ambiguous, especially due to unstable phylogenetic placements of the genera Portevinia and Rhingia. We recovered most subgenera of Cheilosia as monophyletic clades. Dynamic alignment, using the optimization alignment program POY, always recovered more parsimonious topologies under all parameter weighting schemes, than did parsimony analyses using static alignment and analyzed with NONA.     

The phylogeny of early eureptiles: comparing parsimony and Bayesian approaches in the investigation of a basal fossil clade

For the first time the phylogenetic relationships of early eureptiles, consisting of captorhinids, diapsids, and protorothyridids, are investigated in a modern phylogenetic context using both parsimony and Bayesian approaches. Ninety parsimony-informative characters and 25 taxa were included in the analyses. The Bayesian analysis was run with and without a gamma-shape parameter allowing for variable rates across characters. In addition, we ran two more Bayesian analyses that included 42 autapomorphies and thus parsimony-uninformative characters in order to test the effect of variable branch lengths. The different analyses largely converged to the same topology, suggesting that the "protorothyridid" Coelostegus is the sister taxon of all other eureptiles and that the remaining "protorothyridids" are paraphyletic. Also, there is a close relationship between diapsids and Anthracodromeus, Cephalerpeton, and Protorothyris, a grouping of Thuringothyris with captorhinids, and a variable position of the "protorothyridids" Brouffia, Hylonomus, and Paleothyris. The lack of resolution in some parts of the tree might be due to "hard polytomies" and short divergence times between the respective taxa. The tree topology is consistent with the hypothesis that the temporal fenestrations of diapsid reptiles appear to be the consequence of a more lightly built skeleton, indicating a significant ecological shift in the early stages of diapsid evolution. Bayesian analysis is a very useful additional approach in studies of fossil taxa in which more traditional statistical support like the bootstrap is often weak. However, the exclusive use of the Mk model appears suitable only if autapomorphic characters are included, whereas the Mk+gamma model performed well with or without autapomorphies.     

Phylogenetic relationships among the Lorisoidea as indicated by craniodental morphology and mitochondrial sequence data

The phylogeny of the Afro-Asian Lorisoidea is controversial. While postcranial data attest strongly to the monophyly of the Lorisidae, most molecular analyses portray them as paraphyletic and group the Galagidae alternately with the Asian or African lorisids. One of the problems that has bedevilled phylogenetic analysis of the group in the past is the limited number of taxa sampled for both ingroup families. We present the results of a series of phylogenetic analyses based on 635 base pairs (bp) from two mitochondrial genes (12S and 16S rRNA) with and without 36 craniodental characters, for 11 galagid and five lorisid taxa. The outgroup was the gray mouse lemur (Microcebus murinus). Analyses of the molecular data included maximum parsimony (MP), neighbor joining (NJ), maximum likelihood (ML), and Bayesian methods. The model-based analyses and the combined "molecules+morphology" analyses supported monophyly of the Lorisidae and Galagidae. The lorisids form two geographically defined clades. We find no support for the taxonomy of Galagidae as proposed recently by Groves [Primate Taxonomy, Washington, DC: Smithsonian Institution Press. 350 p, 2001]. The taxonomy of Nash et al. [International Journal of Primatology 10:57-80, 1989] is supported by the combined "molecules+morphology" analysis; however, the model-based analyses suggest that Galagoides may be an assemblage of species united by plesiomorphic craniodental characters.