Morphological phylogenetic analysis of Ophrys (Orchidaceae): insights from morpho‐anatomical floral traits into the interspecific relationships in an unresolved clade

Reconstructing the phylogeny of the sexually deceptive orchid genus Ophrys is crucial to our understanding of the evolution of its complex floral morphology. Molecular phylogenetic analyses showed that section Pseudophrys forms a well supported clade with Ophrys bombyliflora, O. tenthredinifera and O. speculum, but were unable to elucidate the relationships between these four groups of taxa. Here we conduct a morphological phylogenetic analysis of this unresolved clade of Ophrys based on a data matrix of 45 macro‐ and micromorphological and anatomical floral characters, using maximum parsimony and Bayesian inference. Our cladistic analysis yielded a single most parsimonious tree and a Bayesian 50% majority‐rule consensus tree which differed in their overall topology but agreed that O. tenthredinifera and O. bombyliflora are not sister groups. The phylogenetic placement of O. tenthredinifera was ambiguous since it shares six valid synapomorphies each with the cluster of O. speculum–O. bombyliflora and with section Pseudophrys. In contrast, O. bombyliflora is most likely the sister group to O. speculum, a finding that rejects an earlier morphological phylogenetic hypothesis and favours the existing molecular trees based on nuclear ITS rather than plastid data. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 454–476.     

Evolution of sperm morphology in potamid freshwater crabs (Crustacea: Brachyura: Potamoidea)

We investigated sperm cells and spermatophores of four species of Old World freshwater crabs belonging to three different genera of the subfamily Potaminae (family Potamidae). Characters previously believed to be apomorphic for the potamid subfamily Potamiscinae were also found to occur in the Potaminae. To infer the morphological ancestral character state combination of the Potamidae, ancestral character state analysis of four different sperm traits was performed, based on a 16S rDNA phylogeny of the investigated species. Comparing molecular phylogeny and character state distribution, several cases of convergent evolution could be identified. The densely packed, coenospermic spermatophores and the occurrence of a ‘tongue‐and‐groove’ connection between operculum and acrosomal zones are probably apomorphies for the whole Potamidae. The spermatozoa of Socotrapotamon socotrense show several unique characters. We also analysed the evolution of acrosome size. The sperm cells of the Potamidae and their sister‐group Gecarcinucidae only slightly overlap in acrosome size. Within the investigated species, the ‘East Asia’ subclade (subfamily Potamiscinae) developed significantly larger acrosomes than the subfamily Potaminae. Our results suggest that the use of brachyuran acrosome morphology for phylogenetic inference at the family level is strongly affected by small sample size, and by convergent character evolution. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010.     

Continuous characters in phylogenetic analyses: patterns of corolla tube length evolution in Lithospermum L. (Boraginaceae)

The present study comprises an analysis of six different scoring schemes and eight different types of analytic methods aiming to investigate the evolution of a continuous character (i.e. corolla tube length) in Lithospermum L. (Boraginaceae). Corolla tube length in the genus is quite variable, ranging from 1 mm to 75 mm, and the length of the corolla tube has implications for pollination biology, such as longer corolla tubes (> 25 mm in length) being pollinated by hummingbirds or moths. In general, the various methods resolve similar ancestral character states; however, different states are reconstructed at nodes in which the descendants greatly differ in corolla tube length. Additionally, it is suggested that all of the variation of a continuous character should be included in analyses, and this may necessitate multiple analyses with different partitions of the data. The various analyses provide evidence that two maximum parsimony methods, linear parsimony and the TNT method, minimize the number of different rates of evolution. In Lithospermum, six origins of corolla tubes > 20 mm in length are resolved, and these origins occurred at two different times periods: (1) in the shadow of hummingbird diversification in North America (approximately 6–8 Mya) and (2) more recently (approximately 1–1.5 MyA). Four substantial decreases in corolla tube length also are reconstructed, and these may be associated with the origin of self‐pollination. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Is evolution faster at ecotones? A test using rates and tempo of diet transitions in Neotropical Sigmodontinae (Rodentia,Cricetidae)

We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tip‐based metrics of trait evolution – Transition Rates, Stasis Time, and Last Transition Time – which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip‐based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space.     

EXAMINING TWO STANDARD ASSUMPTIONS OF ANCESTRAL RECONSTRUCTIONS: REPEATED LOSS OF DICHROMATISM IN DABBLING DUCKS (ANATINI)

Although phylogenetic reconstruction of ancestral character states is becoming an increasingly common technique for studying evolution, few researchers have assessed the reliability of these reconstructions. Here I test for congruence between a phylogenetic reconstruction and a widely accepted scenario based on independent lines of evidence. I used Livezey's (1991) phylogeny to reconstruct ancestral states of plumage dichromatism in dabbling ducks (Anatini). Character state mapping reconstructs monochromatic ancestors for the genus Anas as well as most of its main clades. This reconstruction differs strongly from the widely accepted scenario of speciation and plumage evolution in the group (e.g., Delacour and Mayr 1945; Sibley 1957). This incongruence may occur because two standard assumptions of character state reconstruction are probably not met in this case. Violating either of these two assumptions would be a source of error sufficient to create misleading reconstructions. The first assumption that probably does not apply to ducks is that terminal taxa, in this case species, are monophyletic. Many of the widespread dichromatic species of ducks may be paraphyletic and ancestral to isolated monochromatic species. Three lines of evidence support this scenario: population-level phylogenies, biogeography, and vestigial plumage patterns. The second assumption that probably does not apply to duck plumage color is that gains and losses of character states are equally likely. Four lines of evidence suggest that dichromatic plumage might be lost more easily than gained: weak female preferences for bright male plumage, biases toward the loss of sexually dichromatic characters, biases toward the loss of complex characters, and repeated loss of dichromatism in other groups of birds. These seven lines of evidence support the accepted scenario that widespread dichromatic species repeatedly budded off isolated monochromatic species. Drift and genetic biases probably caused the easy loss of dichromatism in ducks and other birds during peripatric speciation. In order to recover the accepted scenario using Livezey's tree, losses of dichromatism must be five times more likely than gains. The results of this study caution against the uncritical use of unordered parsimony as the sole criterion for inferring ancestral states. Detailed population-level sampling is needed and altered transformation weighting may be warranted in ducks and in many other groups and character types with similar attributes.     

Macrophylogenetic analyses of the gain and loss of self-incompatibility in the Asteraceae

The self-incompatibility (SI) status of 571 taxa from the Asteraceae was identified and the taxa were scored as having SI, partial SI or self-compatibility (SC) as their breeding system. A molecular phylogeny of the internal transcribed spacer (ITS) region was constructed for 211 of these taxa. Macrophylogenetic methods were used to test hypotheses concerning the ancestral state of SI in the Asteraceae, the gain and loss of SI, the irreversibility of the loss of SI and the potential for partial SI or SC to be terminal states. The ancestral breeding system in the family could not be resolved. Both maximum likelihood and parsimony analyses indicated that transitions among all breeding system states provide the best fit to the data and that neither partial SI nor SC is a terminal state. Furthermore, the data indicated that the loss of SI is not irreversible, although breeding system evolution has been more dynamic in some clades than in others. These results are discussed within the context of evidence for the gain and loss of SI, the evolutionary role of partial SI and methodological assumptions of tests of breeding system evolution.     

Contrasting phylogenetic signals and evolutionary rates in floral traits of Neotropical lianas

The diversity of floral forms has long been considered a prime example of radiation through natural selection. However, little is still known about the evolution of floral traits, a critical piece of evidence for the understanding of the processes that may have driven flower evolution. We studied the pattern of evolution of quantitative floral traits in a group of Neotropical lianas (Bignonieae, Bignoniaceae) and used a time‐calibrated phylogeny as basis to: (1) test for phylogenetic signal in 16 continuous floral traits; (2) evaluate the rate of evolution in those traits; and (3) reconstruct the ancestral state of the individual traits. Variation in floral traits among extant species of Bignonieae was highly explained by their phylogenetic history. However, opposite signals were found in floral traits associated with the attraction of pollinators (calyx and corolla) and pollen transfer (androecium and gynoecium), suggesting a differential role of selection in different floral whorls. Phylogenetic independent contrasts indicate that traits evolved at different rates, whereas ancestral character state reconstructions indicate that the ancestral size of most flower traits was larger than the mean observed sizes of the same traits in extant species. The implications of these patterns for the reproductive biology of Bignonieae are discussed. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 378–390.     

Diversity and evolution of male secondary sexual characters in African squeakers and long-fingered frogs

The African frog genera Arthroleptis and Cardioglossa are unique among vertebrates in having males with extremely long third fingers. In some species, this sexual dimorphism is impressive, with male third fingers approaching 40% of body length. However, the diversity of this trait has not been documented thoroughly and several species appear to lack this trait. The present study documents the diversity of male secondary sexual traits in Arthroleptis and Cardioglossa , including elongate third fingers and digital and inguinal spines. Furthermore, it explores hypotheses of trait evolution, including explanations for the absence of male traits. Analyses of covariance suggest that the functional relationship between finger length and snout–vent length (SVL), both within and among species, is different for male finger III than for male fingers I, II, and IV, or for female finger III. Ancestral state reconstruction suggests that all male traits were present in the most recent common ancestor of Arthroleptis and Cardioglossa and that reduction or loss of traits occurred later. Across species, independent contrast analyses find no correlation between SVL and either male relative third digit length or dimorphism in relative third digit length. The number of spines on male fingers II and III are positively correlated but spine number is not correlated with SVL and only weakly correlated with relative third digit length. The diversity of male traits is evolutionarily labile and is not explained by simple hypotheses of character evolution. Arthroleptis and Cardioglossa may thus provide an interesting study system for understanding how changes in sexual selection forces produce male trait diversity.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 553–573.     

Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia)

Cnidarians are early-diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re-evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt-genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt-genomes of members of eight of nine zoantharian families. Although all examined mt-genomes had the same gene order arrangement, there were variations among mt-genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt-DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt-genome protein-coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An “early” transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher-level phylogeny and taxonomy of Zoantharia.     

Evolution of the premaxillary fraenum and substratum in snubnose darters and allies (Percidae: Etheostoma)

Darters (Percidae: Etheostomatinae), a species‐rich group of North American freshwater fishes, vary in the presence of a premaxillary fraenum, a strip of skin that connects the premaxillary bones to the snout, and it is hypothesized that this trait is a trophic adaptation to particular substrata. Ancestral state reconstructions and analyses of phylogenetic associations between presence of the premaxillary fraenum and preferred stream substratum were conducted in a clade of closely related darters (snubnose darters and allies) that vary in morphology and habitat preferences. The most recent common ancestor of this clade was inferred to possess a fraenum and to inhabit rocky substrata, consistent with previous hypotheses, but a significant correlation between fraenum presence and substratum type across the phylogeny was not found.     

Are diminutive turtles miniaturized? The ontogeny of plastron shape in emydine turtles

Miniaturization, or the evolution of a dramatically reduced body size compared to related lineages, is an extraordinarily widespread phenomenon among metazoans. Evolutionary biologists have been fascinated by miniaturization because this transition has occurred numerous times, often among close relatives, providing a model system for studying convergent evolution and its underlying mechanisms. Much of the developmental work describing the ontogeny of miniature species suggests that paedomorphosis is the predominant avenue of miniaturization. Nevertheless, specific alterations to ontogeny appear highly variable, so that even related lineages with similar miniaturized traits produce those similarities via distinct ontogenetic paths. One major vertebrate group that has been overlooked in research on miniaturization is turtles. In the present study, we examined patterns of shape change in the plastron (the ventral part of the shell) over the course of ontogeny in a small clade of turtles (Emydinae) aiming to investigate whether two independently evolved diminutive members of the clade (Glyptemys muhlenbergii and Clemmys guttata) should be considered as miniaturized. We employ geometric morphometric methods to quantify the patterns of shape change these potentially miniaturized species and their relatives undergo during ontogeny, and use molecular phylogenetic trees to reconstruct ancestral conditions and provide information on the polarity of shape changes. We find that differing changes in ontogenetic parameters relative to ancestral conditions accompany the evolution of small size in emydines: G. muhlenbergii changes the duration of ontogeny and rate of shape change, whereas C. guttata changes growth rate. The observed ontogenetic repatterning of these species is reminiscent of changes in ontogeny and life history often found in miniaturized taxa. However, we conclude that C. guttata and G. muhlenbergii are not truly miniaturized because they still produce typical adult shell morphologies, and larger emydines display comparable ontogenetic flexibility. Because no emydines carry juvenile shell features forward into adulthood, we speculate that few, if any turtles, will show paedomorphic shell traits without corresponding changes in defensive strategy because such shells may offer insufficient protection. © 2013 The Linnean Society of London     

Evolution of venom delivery structures in madtom catfishes (Siluriformes: Ictaluridae)

The use of venom to subdue prey or deter predators has evolved multiple times in numerous animal lineages. Catfishes represent one of the most easily recognized, but least studied groups of venomous fishes. Venom glands surround spines on the dorsal and pectoral fins that serve as venom delivery structures. Species of madtom catfishes in the genus Noturus were found to each have one of four venom delivery morphologies: (1) smooth spine with no venom gland; (2) smooth spine with venom gland associated with shaft of spine; (3) serrated spine with venom gland associated with shaft of spine; and (4) serrated spine with venom gland associated with shaft of spine and posterior serrations. Analyses accounting for the phylogenetic history of Noturus species suggest that a serrated pectoral spine with a venom gland is the ancestral condition for the genus. The presence of serrations and a venom gland have been largely conserved among Noturus species, but sting morphology has changed at least five times within the genus. Four of these changes have resulted in a loss of morphological complexity, including the loss of posterior serrations, loss of venom glands associated with the posterior serrations, and one complete loss of the venom gland. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 115–129.     

Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae)

There has been considerable debate regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from proposed candidate loci on a common set of samples. In this study, we evaluated main candidate plastid regions (rpoC1, rpoB, accD) and additional plastid markers (psbB, psbN, psbT exons and the trnS-trnG spacer) as well as the nuclear ribosomal spacer region (ITS1-5.8S-ITS2) in a group of land plants belonging to the mahogany family, Meliaceae. Across these samples, only ITS showed high levels of resolvability. Interspecific sharing of sequences from individual plastid loci was common. The combination of multiple loci did not improve performance. DNA barcoding with ITS alone revealed cryptic species and proved useful in identifying species listed in Convention on International Trade of Endangered Species appendixes.     

Untangling the assassin's web: Phylogeny and classification of the spider-associated Emesine complex (Hemiptera: Reduviidae)

Web-building spiders are formidable predators, yet assassin bugs in the Emesine Complex (Hemiptera: Reduviidae: Emesinae, Saicinae, and Visayanocorinae) prey on spiders. The Emesine Complex comprises >1000 species and these web-associated predatory strategies may have driven their diversification. However, lack of natural history data and a robust phylogenetic framework currently preclude tests of this hypothesis. We combine Sanger (207 taxa, 3865 bp) and high-throughput sequencing data (15 taxa, 381 loci) to generate the first taxon- and data-rich phylogeny for this group. We discover rampant paraphyly among subfamilies and tribes, necessitating revisions to the classification. We use ancestral character state reconstructions for 40 morphological characters to identify diagnostic features for a revised classification. Our new classification treats Saicinae Stål and Visayanocorinae Miller as junior synonyms of Emesinae Amyot and Serville, synonymizes the emesine tribes Ploiariolini Van Duzee and Metapterini Stål with Emesini Amyot and Serville, and recognises six tribes within Emesinae (Collartidini Wygodzinsky, Emesini, Leistarchini Stål, Oncerotrachelini trib.n. , Saicini Stål stat.n. , and Visayanocorini Miller stat.n. ). We show that a pretarsal structure putatively involved in web-associated behaviours evolved in the last common ancestor of Emesini, the most species-rich clade within Emesinae, suggesting that web-associations could be widespread in Emesinae.     

Floral morphology and embryo sac development in Burretiodendron kydiifolium Y. C. Hsu et R. Zhuge (Tiliaceae) and their systematic significance

Phylogenetic analysis of rbc L and atp B gene sequences from Biebersteinia Stephan (represented by B. orphanidis Boiss.) and from selected taxa of the rosids I and II clades does not support traditional grouping of this genus in Geraniaceae s. s. nor in Geraniales, but indicates strong support for a position nested within Sapindales (as recently delimitated). The rbc L and atp B phylogenies obtained were congruent but differently resolved and do not link Biebersteinia to any other clade within Sapindales. Biebersteinia is on a long branch on its own which, given the particular combination of apomorphic morphological characters, justifies familial status.     

Evolutionary history of the arid climate‐adapted Helichrysum (Asteraceae: Gnaphalieae): Cape origin and association between annual life‐history and low chromosome numbers

The basal grade of the large, widely‐distributed Helichrysum‐Anaphalis‐Pseudognaphalium (HAP) clade (Asteraceae, Gnaphalieae) comprises exclusively southern African taxa. These species possess unusual trait combinations relative to the remaining species (a high proportion of annuals, unusual capitulum arrangement, and low base chromosome numbers). A time‐proportional Bayesian phylogenetic hypothesis is generated from nuclear ribosomal sequences from 110 accessions. Ancestral area, life history, and base chromosome number are reconstructed using maximum likelihood, and correlations between life‐history and chromosome number are tested in a phylogenetic framework. The results show that the HAP clade probably originated and experienced initial diversification in the Greater Cape Floristic Region in the Early to Middle Miocene. The ancestor of the HAP clade is inferred to have been perennial with x = 7 base chromosome number. Several independent acquisitions of the annual life‐history are inferred, accompanied by reductions to x = 4 and 5. A single reversal to perennial life history is associated with a subsequent change back to the state of x = 7. Origin and early diversification within the HAP clade follows the pattern of multi‐area seeded radiations within southern Africa, with subsequent migrations to the rest of Africa and the Northern Hemisphere. Occupation of drier habitats with shorter growing seasons may select for the acquisition of a shorter life‐cycle, and our results indicate a strong association between short life‐cycle and reduced chromosome number.     

Evolution of the male genitalia in the genus Limnebius Leach, 1815 (Coleoptera,Hydraenidae)

We investigated the evolution of the male genitalia of species of Limnebius (Coleoptera, Hydraenidae). This genus is very homogeneous externally but characterized by highly diverse male genitalia, which are in some cases extraordinarily complex. We reconstructed a molecular phylogeny for 70 of the c. 150 known species of the genus with six fragments of mitochondrial and nuclear genes. We found two main lineages of Miocene origin, largely corresponding to the synonymized subgenera Bilimneus and Limnebius, which are here re‐erected. Within the Holarctic Limnebius s.s. we found four well‐supported lineages, although with poorly supported relationships between them: the L. piceus, L. gracilipes, L. parvulus and L. nitidus species groups. We describe the aedeagus and its different appendages in detail based on the study of 116 species, including serial histological sections to reconstruct the internal structure of seven of them. Using Bayesian methods we reconstructed the ancestral Limnebius as having small males (c. 1.2 ± 0.5 mm), with a small aedeagus (c. 0.4 ± 0.3 mm) with a free left paramere, probably an externally fused right paramere, and a possible additional appendage. The species of Bilimneus experienced a reduction in size and a simplification of their genitalia, without free parameres and with a very simple, homogenous structure. Within Limnebius s.s. several independent increases in male body and genital size took place, with a strong correlation as measured with independent contrasts. There was, however, no overall correlation between genital size and number of appendages, even though smaller genitalia tend to be less complex.     

Evolution of habitat preference in 243 species of Bent‐toed geckos (Genus Cyrtodactylus Gray, 1827) with a discussion of karst habitat conservation

Understanding the processes that underpin adaptive evolutionary shifts within major taxonomic groups has long been a research directive among many evolutionary biologists. Such phenomena are best studied in large monophyletic groups that occupy a broad range of habitats where repeated exposure to novel ecological opportunities has happened independently over time in different lineages. The gekkonid genus Cyrtodactylus is just such a lineage with approximately 300 species that range from South Asia to Melanesia and occupy a vast array of habitats. Ancestral state reconstructions using a stochastic character mapping analysis of nine different habitat preferences were employed across a phylogeny composed of 76% of the known species of Cyrtodactylus. This was done in order to ascertain which habitat preference is the ancestral condition and from that condition, the transition frequency to more derived habitat preferences. The results indicate that a general habitat preference is the ancestral condition for Cyrtodactylus and the frequency of transitioning from a general habitat preference to anything more specialized occurs approximately four times more often than the reverse. Species showing extreme morphological and/or ecological specializations generally do not give rise to species bearing other habitat preferences. The evolution of different habitat preferences is generally restricted to clades that tend to occur in specific geographic regions. The largest radiations in the genus occur in rocky habitats (granite and karst), indicating that the transition from a general habitat preference to a granite or karst‐dwelling life style may be ecologically uncomplicated. Two large, unrelated clades of karst‐associated species are centered in northern Indochina and the largest clade of granite‐associated species occurs on the Thai‐Malay Peninsula. Smaller, independent radiations of clades bearing other habitat preferences occur throughout the tree and across the broad distribution of the genus. With the exception of a general habitat preference, the data show that karst‐associated species far out‐number all others (29.6% vs. 0.4%–10.2%, respectively) and the common reference to karstic regions as “imperiled arcs of biodiversity” is not only misleading but potentially dangerous. Karstic regions are not simply refugia harboring the remnants of local biodiversity but are foci of speciation that continue to generate the most speciose, independent, radiations across the genus. Unfortunately, karstic landscapes are some of the most imperiled and least protected habitats on the planet and these data continue to underscore the urgent need for their conservation.