Phylogeny of ladybirds (Coleoptera: Coccinellidae): Are the subfamilies monophyletic?

The Coccinellidae (ladybirds) is a highly speciose family of the Coleoptera. Ladybirds are well known because of their use as biocontrol agents, and are the subject of many ecological studies. However, little is known about phylogenetic relationships of the Coccinellidae, and a precise evolutionary framework is needed for the family. This paper provides the first phylogenetic reconstruction of the relationships within the Coccinellidae based on analysis of five genes: the 18S and 28S rRNA nuclear genes and the mitochondrial 12S, 16S rRNA and cytochrome oxidase subunit I (COI) genes. The phylogenetic relationships of 67 terminal taxa, representative of all the subfamilies of the Coccinellidae (61 species, 37 genera), and relevant outgroups, were reconstructed using multiple approaches, including Bayesian inference with partitioning strategies. The recovered phylogenies are congruent and show that the Coccinellinae is monophyletic but the Coccidulinae, Epilachninae, Scymninae and Chilocorinae are paraphyletic. The tribe Chilocorini is identified as the sister-group of the Coccinellinae for the first time.     

Genome‐wide survey of nuclear protein‐coding markers for beetle phylogenetics and their application in resolving both deep and shallow‐level divergences

Beetles (Coleoptera) are the most diverse and species‐rich insect group, representing an impressive explosive radiation in the evolutionary history of insects, and their evolutionary relationships are often difficult to resolve. The amount of ‘traditional markers’ (e.g. mitochondrial genes and nuclear rDNAs) for beetle phylogenetics is small, and these markers often lack sufficient signals in resolving relationships for such a rapidly radiating lineage. Here, based on the available genome data of beetles and other related insect species, we performed a genome‐wide survey to search nuclear protein‐coding (NPC) genes suitable for research on beetle phylogenetics. As a result, we identified 1470 candidate loci, which provided a valuable data resource to the beetle evolutionary research community for NPC marker development. We randomly chose 180 candidate loci from the database to design primers and successfully developed 95 NPC markers which can be PCR amplified from standard genomic DNA extracts. These new nuclear markers are universally applicable across Coleoptera, with an average amplification success rate of 90%. To test the phylogenetic utility, we used them to investigate the backbone phylogeny of Coleoptera (18 families sampled) and the family Coccinellidae (39 species sampled). Both phylogenies are well resolved (average bootstrap support >95%), showing that our markers can be used to address phylogenetic questions of various evolutionary depth (from species level to family level). In general, the newly developed nuclear markers are much easier to use and more phylogenetically informative than the ‘traditional markers’, and show great potential to expedite resolution of many parts in the Beetle Tree of Life.     

Mitogenomic phylogeny of the Naticidae (Gastropoda: Littorinimorpha) reveals monophyly of the Polinicinae

The Naticidae is a species-rich family of predatory marine gastropods with substantial interspecific morphological diversity. The classification of the Naticidae has been traditionally based on morphology data, but the phylogenetic relationships within the family are debated due to conflicting molecular results, especially regarding the monophyly of subfamilies Polinicinae and Naticinae. To further resolve the phylogenetic controversies within the Naticidae, we undertake a phylogenetic approach using 14 newly sequenced complete or nearly complete (only lacking a control region) mitochondrial genomes. Both the maximum likelihood and Bayesian inference analyses supported monophyly of the Polinicinae, but paraphyly of the Naticinae due to the placement of the enigmatic genus Notocochlis. The ancestral character reconstruction suggests that the operculum, a character that currently defines the two subfamilies, evolved from an ancestor with a calcareous operculum in the evolutionary history of naticids. In addition, the chronogram estimates that naticids was originated in late Triassic (about 227 million years ago), consistent with previous hypotheses. Our study highlights the importance of using complete mitochondrial genomes while reconstructing phylogenetic relationships within the Naticidae. The evolution scenario of the naticid operculum contributes new insights into the classification of Naticidae.     

Looks can deceive: Molecular phylogeny of a family of flatworm ectoparasites (Monogenea: Capsalidae) does not reflect current morphological classification

The morphological based taxonomy of highly derived parasite groups is likely to poorly reflect their evolutionary relationships. The taxonomy of the monogenean family Capsalidae, which comprises approximately 180 species of flatworm parasites that predominantly attach to external surfaces of chondrichthyan and teleost fishes, is based mainly on six morphological characters. The phylogenetic history of the family is largely unknown. We reconstructed the phylogenetic relationships of 47 species in 20 genera from eight of the nine subfamilies, from nucleotide sequences of three unlinked nuclear genes, 28S ribosomal RNA, Histone 3 and Elongation Factor 1 α. Our phylogeny was well corroborated, with 75% of branches receiving strong support from both Bayesian posterior probabilities and maximum likelihood bootstrap proportions and all nodes showed positive partitioned likelihood support for each of the three genes. We found that the family was monophyletic, with the Gyrodactylidae and Udonellidae forming the sister group. The Capsalinae was monophyletic, however, our data do not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Entobdella, Listrocephalos, Neobenedenia and Tristoma, but Benedenia and Neoentobdella were polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on the molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification shows little correspondence with the phylogenetic relationships within the family.     

Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

Cerambycidae is a species‐rich family of mostly wood‐feeding (xylophagous) beetles containing nearly 35 000 known species. The higher‐level phylogeny of C erambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher‐level phylogeny of C erambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample (31 C hrysomeloidea, four outgroup taxa: two C urculionoidea and two C ucujoidea) included exemplars of all families and 23 of 30 subfamilies of C hrysomeloidea (18 of 19 non‐chrysomelid C hrysomeloidea), with a focus on the large family C erambycidae. Our results reveal a monophyletic C erambycidae s.s. in all but one analysis, and a polyphyletic C erambycidae s.l. When monophyletic, C erambycidae s.s. was sister to the family D isteniidae. Relationships among the subfamilies of C erambycidae s.s. were also recovered with strong statistical support except for C erambycinae being made paraphyletic by Dorcasomus A udinet‐S erville (D orcasominae) in the nucleotide (but not amino acid) trees. Most other chrysomeloid families represented by more than one terminal taxon – C hrysomelidae, D isteniidae, V esperidae and O rsodacnidae – were monophyletic, but M egalopodidae was rendered paraphyletic by Cheloderus G ray (O xypeltidae). Our study corroborates some relationships within C hrysomeloidea that were previously inferred from morphological data, while also reporting several novel relationships. The present work thus provides a robust framework for future, more deeply taxon‐sampled, phylogenetic and evolutionary studies of the families and subfamilies of C erambycidae s.l. and other C hrysomeloidea.     

Evolutionary relationships of trichostrongyloid nematodes (Strongylida) inferred from ribosomal DNA sequence data

The evolutionary relationships of 21 species of trichostrongyloid nematodes were determined by use of sequence data of the second internal transcribed spacer of the ribosomal DNA aligned according to secondary structure information. Irrespective of the method of analysis used, the topologies of the phylogenetic trees derived from the molecular data differed with respect to all four hypotheses proposed previously for the evolutionary relationships of the different subfamilies within the Trichostrongylidae based on morphological data. Thus, the molecular data set did not resolve the conflict between the four previous proposals for the subfamilial relationships. Nonetheless, all trees derived from the molecular data showed strong support for the exclusion of the genera Filarinema and Amidostomum from the clade containing the species within the family Trichostrongylidae. This represents a major difference from the most recent proposal of the systematics of the Trichostrongyloidea in which these two genera were included within the Trichostrongylidae. Therefore, the molecular data support an earlier systematic framework in which Filarinema and Amidostomum were considered to be sister groups of the Trichostrongyloidea.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

Dactylogyridae 2022: a meta-analysis of phylogenetic studies and generic diagnoses of parasitic flatworms using published genetic and morphological data

Dactylogyridae is one of the most studied families of parasitic flatworms with more than 1000 species and 166 genera described to date including ecto- and endoparasites. Dactylogyrid monogeneans were suggested as model organisms for host-parasite macroevolutionary and biogeographical studies due to the scientific and economic importance of some of their host lineages. Consequently, an array of phylogenetic research into different dactylogyrid lineages has been produced over the past years but the last family-wide study was published 16 years ago. Here, we provide a meta-analysis of the phylogenetic relationships of Dactylogyridae including representatives of all genera with available molecular data (n = 67). First, we investigate the systematic informativeness of morphological characters widely used to diagnose dactylogyrid genera through a parsimony analysis of the characters, character mapping, and phylogenetic comparative methods. Second, we provide an overview of the current state of the systematics of the family and its subfamilies, and summarise potentially poly- and paraphyletic genera. Third, we elaborate on the implications of taxonomic, citation, and confirmation bias in past studies. Fourth, we discuss host range, biogeographical, and freshwater-marine patterns. We found two well-supported macroclades which we assigned to the subfamilies Dactylogyrinae and Ancyrocephalinae. These subfamilies further include 16 well-supported clades with only a few synapomorphies that could be deduced from generic diagnoses in the literature. Furthermore, few morphological characters considered systematically informative at the genus level display a strong phylogenetic signal. However, the parsimony analysis suggests that these characters provide little information on the relationships between genera. We conclude that a strong taxonomic bias and low coverage of DNA sequences and regions limit knowledge on morphological and biogeographical evolutionary patterns that can be inferred from these results. We propose addressing potential citation and confirmation biases through a ‘level playing field’ multiple sequence alignment as provided by this study.     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades

Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister-group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites+Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus+termites), and a further series of compensatory base changes in this stem-loop is synapomorphic for the Neoisoptera. The complicated repeat structures first identified in Reticulitermes, composed of short (A-type) and long (B-type repeats) defines the clade Heterotermitinae+Termitidae, while the secondary loss of A-type repeats is synapomorphic for the non-macrotermitine Termitidae.     

Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae)

Members of the phlox family (Polemoniaceae) serve as useful models for studying various evolutionary and biological processes. Despite its biological importance, no family-wide phylogenetic estimate based on multiple DNA regions with complete generic sampling is available. Here, we analyze one nuclear and five chloroplast DNA sequence regions (nuclear ITS, chloroplast matK, trnL intron plus trnL-trnF intergeneric spacer, and the trnS-trnG, trnD-trnT, and psbM-trnD intergenic spacers) using parsimony and Bayesian methods, as well as assessments of congruence and long branch attraction, to explore phylogenetic relationships among 84 ingroup species representing all currently recognized Polemoniaceae genera. Relationships inferred from the ITS and concatenated chloroplast regions are similar overall. A combined analysis provides strong support for the monophyly of Polemoniaceae and subfamilies Acanthogilioideae, Cobaeoideae, and Polemonioideae. Relationships among subfamilies, and thus for the precise root of Polemoniaceae, remain poorly supported. Within the largest subfamily, Polemonioideae, four clades corresponding to tribes Polemonieae, Phlocideae, Gilieae, and Loeselieae receive strong support. The monogeneric Polemonieae appears sister to Phlocideae. Relationships within Polemonieae, Phlocideae, and Gilieae are mostly consistent between analyses and data permutations. Many relationships within Loeselieae remain uncertain. Overall, inferred phylogenetic relationships support a higher-level classification for Polemoniaceae proposed in 2000.     

Phylogeny of psychodid subfamilies (Diptera: Psychodidae) inferred from nuclear DNA sequences with a review of morphological evidence for relationships

Psychodidae is a diverse family of flies with approximately 3000 described species in six subfamilies, including Phlebotominae vectors of human disease. Psychodidae has been the subject of few phylogenetic investigations and development of a stable classification has been hampered by poor understanding of the morphology of larvae, pupae and adults. Specimens were collected, and we analysed DNA sequence data from two nuclear genes for one or more representatives of all subfamilies. The subfamilies with multiple representatives included were resolved as monophyletic with good support. Placement of Horaiellinae, Sycoracinae and Trichomyiinae remains unclear, whereas Bruchomyiinae is hypothesized as the sister group to (Phlebotominae + Psychodinae). Representatives of some psychodine tribes were resolved in agreement with previous hypotheses. Relationships among and within subfamilies are discussed, and morphological characters supporting these relationships are reviewed. One compelling synapomorphy of the male genitalia supporting a relationship between Phlebotominae and Psychodinae is the presence of articulated surstyli with apical retinacula. Only cerci are present and sometimes developed into clasping structures in males of other subfamilies.     

Phylogenetic relationships of leptophlebiid mayflies as inferred by histone H3 and 28S ribosomal DNA

Abstract Leptophlebiidae is among the largest and most diverse groups of extant mayflies (Ephemeroptera), but little is known of family‐level phylogenetic relationships. Using two nuclear genes (the D2 + D3 region of 28S ribosomal DNA and histone H3) and maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI), we inferred the evolutionary relationships of 69 leptophlebiids sampled from six continents and representing 30 genera plus 11 taxa of uncertain taxonomic rank from Madagascar and Papua New Guinea. Although we did not recover monophyly of the Leptophlebiidae, monophyly of two of the three leptophlebiid subfamilies, Habrophlebiinae and Leptophlebiinae, was recovered with moderate to strong support in most analyses. The Atalophlebiinae was rendered paraphyletic as a result of the inclusion of members of Ephemerellidae or the Leptophlebiinae clade. For the species‐rich Atalophlebiinae, four groups of taxa were recovered with moderate to strong branch support: (i) an endemic Malagasy clade, (ii) a Paleoaustral group, a pan‐continental cluster with members drawn from across the southern hemisphere, (iii) a group, uniting fauna from North America, southeast Asia and Madagascar, which we call the Choroterpes group and (iv) a group uniting three New World genera, Thraulodes, Farrodes and Traverella. Knowledge of the phylogenetic relationships of the leptophlebiids will aid in future studies of morphological evolution and biogeographical patterns in this highly diverse and speciose family of mayflies.     

Morphology and biogeography of Apiaceae subfamily Saniculoideae as inferred by phylogenetic analysis of molecular data

The phylogenetic placements of several African endemic genera at the base of Apiaceae subfamilies Saniculoideae and Apioideae have revolutionized ideas of relationships that affect hypotheses of character evolution and biogeography. Using an explicit phylogeny of subfamily Saniculoideae, we reconstructed the evolutionary history of phenotypic characters traditionally important in classification, identified those characters most useful in supporting relationships, and inferred historical biogeography. The 23 characters examined include those of life history, vegetative morphology, inflorescences, and fruit morphology and anatomy. These characters were optimized over trees derived from maximum parsimony analysis of chloroplast DNA trnQ-trnK sequences from 94 accessions of Apiaceae. The results revealed that many of these characters have undergone considerable modification and that traditional assumptions regarding character-state polarity are often incorrect. Infrasubfamilial relationships inferred by molecular data are supported by one to five morphological characters. However, none of these morphological characters support the monophyly of subfamilies Saniculoideae or Apioideae, the clade of Petagnaea, Eryngium and Sanicula, or the sister-group relationship between Eryngium and Sanicula . Southern African origins of Saniculoideae and of its tribes Steganotaenieae and Saniculeae are supported based on dispersal-vicariance analysis.     

Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, phylogenetic inference for many lineages dominated by non‐model species has not yet benefited from NGS, which can complement Sanger sequencing studies. One such lineage, whose phylogenetic relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given the lack of consensus on higher‐level relationships and the importance of a robust phylogeny for evolutionary hypothesis testing, we use a large data set comprised of hundreds of ultraconserved element (UCE) loci to infer the phylogeny of Coreoidea (excluding Stenocephalidae and Hyocephalidae), with emphasis on the families Coreidae and Alydidae. We generated three data sets by including alignments that contained loci sampled for at least 50%, 60%, or 70% of the total taxa, and inferred phylogeny using maximum likelihood and summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive phylogenetic analyses of coreoids were also re‐evaluated within our molecular phylogenetic framework. We recovered 439–970 loci per species (16%–36% of loci targeted) and combined this with previously generated UCE data for 12 taxa. All data sets, regardless of analytical approach, yielded topologically similar and strongly supported trees, with the exception of outgroup relationships and the position of Hydarinae. We recovered a monophyletic Coreoidea, with Rhopalidae highly supported as the sister group to Alydidae + Coreidae. Neither Alydidae nor Coreidae were monophyletic; the coreid subfamilies Hydarinae and Pseudophloeinae were recovered as more closely related to Alydidae than to other coreid subfamilies. Coreinae were paraphyletic with respect to Meropachyinae. Most morphological traits were homoplastic with several clades defined by few, if any, synapomorphies. Our results demonstrate the utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and highlight that novel insights may come from such approaches.     

Phylogenetic analysis of Macrobiotidae (Eutardigrada, Parachela): a combined morphological and molecular approach

Combined analyses of morphological and molecular data were used to resolve phylogenetic relationships within Macrobiotidae (Eutardigrada). Morphological data were analysed using a cladistic approach with a matrix comprising 15 taxa with 17 characters to obtain a phylogenetic reconstruction. Molecular data were obtained by sequencing the cytochrome c oxidase subunit I gene in seven species of Macrobiotidae and one of Eohypsibiidae (used as outgroup). The morphological character defining the family, symmetrical claw on each leg, turns out to be plesiomorphic. Moreover, neither morphological nor molecular analyses supports a monophyletic clade for the subfamily Macrobiotinae, whereas both support a well defined evolutionary line (Murrayinae) within the family. We propose elevating the latter to family level (Murrayidae) while temporarily retaining as valid the family Macrobiotidae (amending its diagnosis, including within it only Macrobiotinae). Murrayidae opens an interesting evolutionary prospective, because the entire line has differentiated without sexual reproduction, constituting an example of evolution of asexual lineages.     

Phylogenomic analysis resolves the relationships among net‐winged beetles (Coleoptera: Lycidae) and reveals the parallel evolution of morphological traits

Net‐winged beetles (Coleoptera: Lycidae) are a diverse group of elateroids known for aposematism and neoteny. Phylogenetic analyses of morphological and molecular data have revealed different results with respect to within‐group relationships. In this study, we recovered a highly supported phylogenomic phylogeny and identified seven subfamilies: Dexorinae stat.n. , Calochrominae stat.n. , Erotinae, Ateliinae, Lycinae, Lyropaeinae stat.n. and Metriorrhynchinae stat.n. Our results suggest that female neoteny evolved multiple times. Therefore, the development of similar morphological modifications in neotenics may be linked and may have produced characteristics such as body miniaturization, structural simplification, i.e. reduction of mouthparts, fewer antennomeres and palpomeres, uniquely shaped terminal palpomeres, shortened elytra, the loss of coadaptation between the elytra and pronotum, and others. Additional traits evolved in parallel due to similarities in biology, function and sexual selection. These characteristics include mimetic similarities, the presence of the rostrum, pronotal carinae and elytral costae, and the structure of male genitalia. By comparing the phylogenomic topology with the evolution of morphological characters, we were able to identify evolutionary trends in lycids and compare them with analogues for other neotenic elateroids. These traits have not been accepted as homoplasies due to the ambiguous phylogenetic signal from Sanger sequencing markers.     

Mitochondrial and nuclear markers support the monophyly of Dolichopodidae and suggest a rapid origin of the subfamilies (Diptera: Empidoidea)

Abstract. The Dolichopodidae is a species‐rich dipteran group with almost 7000 described species. The monophyly of the subfamilies and their relationships remain largely unknown because the polarities of key morphological characters are unclear and molecular data are available only for 9 of the 19 proposed subfamilies. Here we test whether molecular data from two nuclear (18S, 28S) and four mitochondrial (12S, 16S, Cytb, COI) genes can resolve the higher‐level relationships within the family. Our study is based on 76 Oriental species from 12 dolichopodid subfamilies and uses eight species of Empididae and Hybotidae as outgroups. Parsimony and likelihood analyses confirm the monophyly of the Dolichopodidae, as well as the monophyly of five of the ten subfamilies represented by more than two species [Sympycninae, Sciapodinae, Dolichopodinae, Hydrophorinae (excluding tribe Aphrosylini), Neurigoninae]. There is strong support for restoring the tribe Aphrosylini as a separate subfamily Aphrosylinae. The monophyly of Medeterinae, Peloropeodinae and Diaphorinae is dependent on which tree reconstruction technique is used, how indels are coded, and whether the fast‐evolving sites are excluded. Overall, we find that our sample of Oriental species is largely compatible with the subfamily concepts that were developed for the northern temperate fauna. However, our data provide little support for relationships between the subfamilies. Branch lengths, saturation, and distance plots suggest that this is probably the result of the rapid origin of dolichopodid subfamilies over a relatively short time. We find that genera that are difficult to place into subfamilies based on morphological characters are generally also difficult to place using molecular data. We predict that a dense, balanced taxon sample and protein‐encoding nuclear genes will be needed to resolve the higher‐level relationships in the Dolichopodidae.     

Molecular phylogeny of grunts (Teleostei, Haemulidae), with an emphasis on the ecology, evolution, and speciation history of New World species

ABSTRACT: BACKGROUND: The fish family Haemulidae is divided in two subfamilies, Haemulinae and Plectorhynchinae (sweetlips), including approximately 17 genera and 145 species. The family has a broad geographic distribution that encompasses contrasting ecological habitats resulting in a unique potential for evolutionary hypotheses testing. In the present work we have examined the phylogenetic relationships of the family using selected representatives of additional Percomorpha based on Bayesian and Maximum likelihood methods by means of three mitochondrial genes. We also developed a phylogenetic hypothesis of the New World species based on five molecular markers (three mitochondrial and two nuclear) as a framework to evaluate the evolutionary history, the ecological diversification and speciation patterns of this group. RESULTS: Mitochondrial genes and different reconstruction methods consistently recovered a monophyletic Haemulidae with the Sillaginidae as its sister clade (although with low support values). Previous studies proposed different relationships that were not recovered in this analysis. We also present a robust molecular phylogeny of Haemulinae based on the combined data of two nuclear and three mitochondrial genes. All topologies support the monophyly of both sub-families (Haemulinae, Plectorhinchinae). The genus Pomadasys was shown to be polyphyletic and Haemulon, Anisotremus, and Plectorhinchus were found to be paraphyletic. Four of seven presumed geminate pairs were indeed found to be sister species, however our data did not support a contemporaneous divergence. Analyses also revealed that differential use of habitat might have played an important role in the speciation dynamics of this group of fishes, in particular among New World species where extensive sample coverage was available. CONCLUSIONS: This study provides a new hypothesis for the sister clade of Hamulidae and a robust phylogeny of the latter. The presence of para- and polyphyletic genera underscores the need for a taxonomic reassessment within the family. A scarce sampling of the Old World Pomadasys species prevents us to definitively point to a New World origin of the sub-familiy Haemulinae, however our data suggest that this is likely to be the case. This study also illustrates how life history habitat influences speciation and evolutionary trajectories.