Congruence between comparative morphology and molecular phylogenies: Evolution of the male genital skeletal/muscular system in the subtribe Polyommatina (Lepidoptera,Lycaenidae)

The skeleton and musculature of male genitalia were studied in species of a model butterfly group (subtribe Polyommatina, Lycaenidae). In total, we analyzed 45 species of the tribe Polyommatini most of which were previously used in the molecular phylogenetic study (Talavera et al., 2013). The studied morphological characters were mapped on the molecular trees, which allowed us to reveal trends of morphological changes and to estimate the age of their origin. As a result, chronology of evolution of skeleton and musculature traits was established. It was shown that periods of slow morphological evolution alternated in the subtribe Polyommatina with those of a high rate of origin of new traits. For example, topography of the intravalvar muscles has not changed for 26 MY preserving their initial fan-shaped attachment. The evolution of intravalvar muscles started 10 MYA, proceeded slowly during the first 5 MY, and then accelerated during the last 5 MY resulting in the extensive splitting of the musculature in most monophyletic lineages. Mapping the morphological characters on the phylogeny demonstrated that the rates of skeleton and muscle evolution within the skeleton/musculature apparatus were different. In most cases the intravalvar musculature evolved much faster than the skeleton. The cladistic interpretation of states of morphological traits was found to be consistent with phylogenetic reconstructions based on analysis of multiple molecular markers. Moreover, morphological synapomorphies were found for the lineages Alpherakya + Glabroculus and Aricia + (Alpherakya + Glabroculus), which had low statistical support in molecular phylogenetic analysis. Additionally, in some cases molecular studies helped to reveal trends in the evolution of morphological traits. For example, the unpaired uncus and the compact juxta are not plesiomorphic for Cupidina as previously thought; instead, they were shown to have evolved secondarily within this subtribe.     

Quantitative and qualitative differences in morphological traits revealed between diploid Fragaria species

BACKGROUND AND AIMS: The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. METHODS: A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. KEY RESULTS: Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. CONCLUSIONS: Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group.     

Hidden biodiversity: total evidence phylogenetics and evolution of morphological traits in a highly diverse lineage of endogean ground beetles,Typhlocharis Dieck, 1869 (Carabidae,Trechinae, Anillini)

Typhlocharis is the most diverse eyeless endogean ground beetle genus known to date, with 62 species all endemic to the West Mediterranean region. The lineage is characterized by a conservative and singular body plan within Carabidae that contrasts with a high morphological diversity in many traits. We provide an exhaustive phylogeny of the lineage through the study of 92 morphological characters from all 62 described species and 45 potential new species from 70 additional populations, and the combination of morphological and available molecular data, in the first total evidence phylogenetic approach for a highly diverse endogean lineage. We tracked the evolution of morphological traits over the obtained phylogenies. Results suggest eight morphologically distinct clades, which do not correspond to the species groups proposed formerly. Ancestral state reconstructions and phylogenetic signal analyses of morphological traits revealed that some of the previously key characters to the classification of Typhlocharis, such as the umbilicate series or the apical denticles of elytra, are highly homoplasic, whereas other characters show stronger phylogenetic signal, including structures in the antennae, gula, pronotum and last abdominal ventrite. This evidence supports the split of Typhlocharis into three genera: Lusotyphlus gen. nov. ; Typhlocharis Dieck, 1869 and Microcharidius Coiffait, 1969 (revalidated), forming the subtribe Typhlocharina Jeanne, 1973.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Character analysis in morphological phylogenetics: problems and solutions

Many aspects of morphological phylogenetics are controversial in the theoretical systematics literature and yet are often poorly explained and justified in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, regardless of whether they are coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (definition, delimitation, and ordering of character states) may have a common solution: coding morphological characters as continuous quantitative traits. A new parsimony method (step-matrix gap-weighting, a modification of Thiele's approach) is proposed that allows quantitative traits to be analyzed as continuous variables. The problem of scaling or weighting quantitative characters relative to qualitative characters (and to each other) is reviewed, and three possible solutions are described. The new coding method is applied to data from hoplocercid lizards, and the results show the sensitivity of phylogenetic conclusions to different scaling methods. Although some authors reject the use of continuous, overlapping, quantitative characters in phylogenetic analysis, quantitative data from hoplocercid lizards that are coded using the new approach contain significant phylogenetic structure and exhibit levels of homoplasy similar to those seen in data that are coded qualitatively.     

Phylogeny of the Baldratiina (Diptera: Cecidomyiidae) inferred from morphological, ecological and molecular data sources, and evolutionary patterns in plant-galler relationships

The phylogeny of the gall-midge subtribe Baldratiina (Diptera: Cecidomyiidae) was reconstructed from molecular (partial sequence of the mitochondrial 12S rDNA), morphological and ecological data sets, using 16 representative species of most of the genera. The morphological and ecological data were combined in a single character matrix and analyzed separately from the molecular data, resulting in an eco-morphological cladogram and a molecular cladogram. Attributes of galls and host associations were superimposed on the molecular cladogram in order to detect possible trends in the evolution of these traits. The cladograms resulting from the two independent analyses were statistically incongruent, although both provide evidence for the monophyly of the genera Baldratia and Careopalpis and the paraphyly of the genera Stefaniola and Izeniola. The results suggest a minor impact of the morphological characters traditionally used in the classification of the Baldratiina, whereas ecological data had a major impact on the phylogenetic inference. Mapping of gall and host attributes on the molecular cladogram suggests that multi-chambered stem galls constitute the ancestral state in the subtribe, with several subsequent shifts to leaf galls. It is concluded that in contrast to other studied groups of gall insects, related baldratiine species induce different types of galls, attesting to speciation driven by gall-type shifts at least as often as host shifts.     

Evolution of male sexual characters in the oriental Drosophila melanogaster species group

Understanding the genetic and molecular mechanisms of morphological evolution is one of the greatest challenges in evolutionary biology. Sexually dimorphic traits, which often evolve at a high rate due to their involvement in mate choice and sexual selection, present unique opportunities for investigating changes in development over short evolutionary distances. Phylogenetic analysis is essential to provide a historical framework for comparative studies of development by establishing the order and polarity of morphological changes. In this report, we apply a new molecular phylogeny to reconstruct the evolution of male sexual characters in a group of species closely related to the model species Drosophila melanogaster. These highly variable traits include wing melanin patterns, the sex comb, and the structure of external genitalia and analia. We show that sexually dimorphic characters can diverge very rapidly among closely related species. More surprisingly, we also find a pervasive pattern of independent origin and secondary loss of male sexual traits in different evolutionary lineages.     

Phylogeny of prickly poppies,Argemone (Papaveraceae), and the evolution of morphological and alkaloid characters based on ITS nrDNA sequence variation

Evolutionary relationships withinArgemone (Papaveraceae) were inferred from nucleotide variation in nuclear ribosomal DNA. A complete representation of the genus was achieved by using herbarium material to a large extent (74%). Four distinct clades can be recognized based on the molecular results. The support for the different clades varies greatly due to a very uneven distribution of characters. Although some clades are largely unresolved, some unexpected relationships, for example the sister group relationship of the relict speciesA. subintegrifolia to the rest ofArgemone, were found. The evolution of morphological and alkaloid characters against the background of the obtained phylogeny is discussed. Whereas the morphological characters provide some support for the phylogeny found, the alkaloid characters turned out not to contain much phylogenetic information. Past difficulties in recognizing phylogenetic relationships withinArgemone result from largely continuous morphological variation and from parallelisms correlated with and probably caused by polyploidization.     

Phylogeny of the Heterodoxus octoseriatus group (Phthiraptera: Boopiidae) from rock-wallabies (Marsupialia: Petrogale)

The phylogenetic position of the Heterodoxus octoseriatus group is inferred from morphological characters. Two character states support monophyly of this group. Another indicates that its sister-group is a group of 11 other Heterodoxus species (here called the H. calabyi group), that infest at least seven other genera of macropodid marsupials. Fourteen potential apomorphies, associated with the male and female genitalia, are identified. Evident rapid and divergent evolution of the genitalia, however, precludes determination of their polarity by comparison with an out-group (the sister-group). Consequently, phylogeny in the H. octoseriatus group is inferred from the close similarity of morphological characters. In light of the phylogenetic analysis and a phenogram, speciation and the evolution of morphological characters in the H. octoseriatus group is discussed.     

Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: multiple origins of bioluminescence and extreme sexual dimorphism

Evolutionists often use phylogeny to examine independent evolutionary events in search of generality. Therefore, groups of organisms rich in such independent character transitions are particularly valuable for the study of evolution. With respect to eyes, vision, and light-related characters, one such group is Ostracoda (Crustacea). Phylogenies of ostracods, derived from DNA sequence data and morphological characters, are presented. These inferred relationships largely agree with previous assessments of ostracod phylogeny, with the exception of paraphyletic Philomedidae. Based on methods of character reconstruction using these inferred relationships, different groups of ostracods probably evolved both bioluminescence and extreme sexual dimorphism (females lack eyes, males have large eyes) multiple times. Furthermore, myodocopid ostracods may have evolved compound eyes independently of other arthropods. For these and other reasons, it is proposed that the Ostracoda are an exceptionally important group for studying the evolution of vision- and light-related characters.     

Molecular phylogenies support multiple morphological reductions in the liverwort subclass Marchantiidae (Bryophyta)

The phylogeny of one of the putative basal-most group of land plants, the Marchantiidae, is estimated with morphological characters and with sequences of the nuclear (LSU) rDNA gene (first four domains of the 5' end of the 26S rRNA and four subsequent regions) from 34 species and 27 genera. Molecular and morphological data display high degrees of incongruence. The molecular tree topology predominates in the combined analysis. A trend from complex towards simpler morphological traits is apparent from the molecular and combined trees, whereas a trend from simple towards complex traits prevails in the morphological tree. Previously published molecular data corroborate the molecular results. It is suggested that the incongruence stems from the presence of coherent sets of reduction-related morphological traits varying in concert in the morphological data. Marchantiidae is traditionally subdivided into Marchantiales, Sphaerocarpales and Monocleales, with the majority of taxa referred to the first group. The molecular and the combined data both indicate unequivocally that Sphaerocarpales and Monocleales are nested within Marchantiales, and this result is not explicitly refuted by the morphological data.     

Evolution and phylogeny of the scarab subtribe Anisopliina (Coleoptera: Scarabaeidae: Rutelinae: Anomalini)

Abstract.  The subtribe Anisopliina (Scarabaeidae: Rutelinae: Anomalini) is associated with grasses, and its species are distributed in the Palaearctic, Oriental, Ethiopian, Nearctic and Neotropical biogeographical regions. Phylogenetic analysis of adult morphological characters was conducted to examine the monophyly and classification of the group, as well as to examine characters associated with grass pollinivory and graminivory. We review the biology, phylogeny and classification of the Anisopliina and provide an overview of each genus. The analysis of ninety-one morphological characters using parsimony does not support the monophyly of the subtribe Anisopliina. Instead, the results provide support for a group referred to here as the anisopliine clade, a circum-Mediterranean group, forming an internal clade within the well-supported tribe Anomalini. Sister group relationships are discussed, possibly being associated with a New World anomaline taxon. Character states associated with grass herbivory, including mouthpart and leg characters, are discussed based on the phylogenetic analysis. Within the Anomalini, an evolutionary shift from generalized leaf feeding to grass associations and grass pollen feeding is supported.     

Character evolution in Hydrozoa (phylum Cnidaria)

The diversity of hydrozoan life cycles, as manifested in the wide range of polyp, colony, and medusa morphologies, has been appreciated for centuries. Unraveling the complex history of characters involved in this diversity is critical for understanding the processes driving hydrozoan evolution. In this study, we use a phylogenetic approach to investigate the evolution of morphological characters in Hydrozoa. A molecular phylogeny is reconstructed using ribosomal DNA sequence data. Several characters involving polyp, colony, and medusa morphology are coded in the terminal taxa. These characters are mapped onto the phylogeny and then the ancestral character states are reconstructed. This study confirms the complex evolutionary history of hydrozoan morphological characters. Many of the characters involving polyp, colony, and medusa morphology appear as synapomorphies for major hydrozoan clades, yet homoplasy is commonplace.     

Molecular phylogenetics of the holly leafminers (Diptera: Agromyzidae: Phytomyza): species limits, speciation, and dietary specialization

A molecular phylogenetic analysis was conducted to determine relationships and to investigate character evolution in the Phytomyza ilicis group of leafmining flies on hollies (Aquifoliaceae: Ilex). A total of 2207 bp of the mitochondrial cytochrome oxidase I and II genes were sequenced for all known holly leafminers, as well as for several undescribed members of this group. Maximum-parsimony analysis of the sequence data indicates that these leafminers form a monophyletic group with the inclusion of an undescribed leafminer that feeds on the distantly related plant Gelsemium sempevirens (Loganiaceae). Species boundaries of previously known and of undescribed holly leafmining species were confirmed with the molecular data, with one exception. Optimization of variable ecological and morphological characters onto the most parsimonious phylogeny suggests that these traits are evolutionarily labile, requiring multiple instances of convergence and/or reversal to explain their evolutionary history. Speciation in holly leafminers is associated with host shifts and appears to involve colonization of new hosts more often than cospeciation as the hosts diverge. Monophagy is the most common feeding pattern in holly leafminers, and more generalized feeding is inferred to have evolved at least two separate times, possibly as a prelude to speciation.     

Phylogeny of Steinernema travassos, 1927 (Cephalobina: Steinernematidae) inferred from ribosomal DNA sequences and morphological characters

Entomopathogenic nematodes in Steinernema, together with their symbiont bacteria Xenorhabdus, are obligate and lethal parasites of insects that can provide effective biological control of some important lepidopteran, dipteran, and coleopteran pests of commercial crops. Phylogenetic relationships among 21 Steinernema species were estimated using 28S ribosomal DNA (rDNA) sequences and morphological characters. Sequences of the rDNA internal transcribed spacers were obtained to provide additional molecular characters to resolve relationships among Steinernema carpocapsae, Steinernema scapterisci, Steinernema siamkavai, and Steinernema monticolum. Four equally parsimonious trees resulted from combined analysis of 28S sequences and 22 morphological characters. Clades inferred from analyses of molecular sequences and combined datasets were primarily reliably supported as assessed by bootstrap resampling, whereas those inferred from morphological data alone were not. Although partially consistent with some traditional expectations and previous phylogenetic studies, the hypotheses inferred from molecular evidence, and those from combined analysis of morphological and molecular data, provide a new and comprehensive framework for evaluating character evolution of steinernematids. Interpretation of morphological character evolution on 6 trees inferred from sequence data and combined evidence suggests that many structural features of these nematodes are highly homoplastic, and that some structures previously used to hypothesize relationships represent ancestral character states.     

An integrative approach identifies developmental sequence heterochronies in freshwater basommatophoran snails

Adopting an integrative approach to the study of sequence heterochrony, we compared the timing of developmental events encompassing a mixture of developmental stages and functional traits in the embryos of 12 species of basommatophoran snails in an explicit phylogenetic framework. PARSIMOV analysis demonstrated clear functional heterochronies associated both with basal branches within the phylogeny and with terminal speciation events. A consensus of changes inferred under both accelerated transformation and delayed transformation optimizations identified four heterochronies where the direction of movement was known plus six twin heterochronies where the relative movements of the two events could not be assigned. On average, 0.5 and 0.58 events were inferred to have changed their position in the developmental sequence on internal and terminal branches of the phylogeny, respectively; these values are comparable with frequencies of sequence heterochrony reported in mammals. Directional heterochronies such as the early occurrence of body flexing in relation to the ontogeny of the eye spots, heart beat, and free swimming events occurred convergently and/or at different levels (i.e., familial, generic, and species) within the phylogeny. Such a functional approach to the study of developmental sequences has highlighted the possibility that heterochrony may have played a prominent role in the evolution of this group of invertebrates.     

Phylogeny of the tribe Fumarieae (Papaveraceae s.l.) based on chloroplast and nuclear DNA sequences: Evolutionary and biogeographic implications

? Premise of the Study: Little research has been done at the molecular level on the tribe Fumarieae (Papaveraceae). Papaveraceae is a model plant group for studying evolutionary patterns despite the lack of a reference phylogeny for this tribe. We investigated the phylogenetic relationships within the tribe to complete the molecular data for this family in order to help understand its character evolution and biogeographic pattern. ? Methods: We used maximum-parsimony and Bayesian approaches to analyze five DNA regions for 25 species representing 10 of the 11 Fumarieae genera and five outgroups. Evolutionary pathways of four characters (habit, life span, type of fruit, and number of seeds per fruit) were inferred on the phylogeny using parsimony. The ancestral distribution areas were reconstructed using dispersal-vicariance analysis. ? Key Results: Fumarieae is monophyletic and includes three groups that agree with the morphology-based subtribes: Discocapninae, Fumariinae, and Sarcocapninae. Within subtribes, the relationships among genera were different from those obtained with morphological data. Annual life span, nonchasmophytic habit, and a several-seeded capsule were the basal character states for the tribe. The ancestor occupied a continuous area between West Eurasia and Africa. Vicariances explain the divergence between lineages Discocapninae (South Africa) and Fumariinae-Sarcocapninae (Mediterranean), and the disjunction of Fumariinae (Mediterranean-Central Asia). ? Conclusions: Molecular phylogeny confirms the subtribal classification of Fumarieae based on morphology. However it provides different results regarding the relationships among genera within each subtribe, which affects the inference of the evolutionary pathway followed by the four selected characters. The disjunct distribution of the tribe is explained by different vicariance scenarios.     

Phylogeny of the Gardenieae (Rubiaceae)

The phylogeny of Gardenieae (Rubiaceae) is evaluated using 70 morphological and anatomical characters and 81 terminal taxa. After successive reweighting of the characters and modified bootstrap tests the following is concluded. The position of the Diplosporinae genera Argocoffeopsis, Calycosiphonia, Cremaspora and Tricalysia with the genera belonging to the tribes Aulacocalyceae, Coffeeae, Octotropideae and Pavetteae, suggests that this subtribe does not belong in Gardenieae. Posoqueria is nested among outgroup genera and consequently is not a member of the tribe. Robbrecht & Puff's informal 'tetrad group' is monophyletic. Likewise, their 'Alibertia group' is supported as monophyletic, although slightly rearranged. On the other hand, their 'Aidia group' must he greatly expanded with several genera in order to be monophyletic, but the monophyly of this group is weakly supported. Several disputed genera should be included in Gardenieae ( Anomanthodia, Amaioua, Brachytome , and supposedly Bertiera ). Most inferred groups, however, exhibit low bootstrap values and should he viewed with caution.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.