Comparative biology and the importance of cladistic classification: a case study from the sensory biology of squamate reptiles

Evolutionary taxonomy has all but succumbed to cladistic methodology, but it continues to exert considerable influence in the realm of higher classification. Some systematists accept cladistic methods in phylogeny inference, but allow paraphyly in formal classifications. Most important, however, many traditional classifications based on paraphyletic groups (e.g. 'Reptilia') remain in force, deeply entrenched in the literature. Cladists have argued that such paraphyletic classifications can mislead comparative biologists into false evolutionary generalizations, but this assertion has rarely, if ever, been supported by example. This paper provides a case study, illustrating in detail the influence of a traditional paraphyletic classification of squamate reptiles on the historical development of ideas regarding the evolution of sensory modes (chemoreception vs. vision) in the group. The paraphyletic classification is shown to have led to false generalizations and incorrect conclusions stemming directly from the fact that the classification did not reflect accurately the phylogeny of Squamata, particularly the cladistic relationships of Gekkota. This study provides direct evidence that evolutionary generalization must be rooted in the branching pattern of phylogeny and not the potentially arbitrary categorical ranks of traditional taxonomies. It further supports recent calls for a truly phylogenctic taxonomy that has as its philosophical core the concept of descent.     

有鳞目系统发生研究进展

有鳞目是现存爬行动物中种类最多的一类,分布遍及世界各地,形态多样,其一直被广泛应用于生态学、生物地理学及探讨物种进化的研究。但到目前为止有鳞目内部的系统发生关系一直存在许多争议。综述了采用古生物学、形态学、分子生物学等研究方法所提出的有鳞目系统发生关系的多种观点,以期为该类动物的系统发生研究提供参考资料。     

Comparative morphology of mandibular structures in lycid larvae and its phylogenetic implications (Polyphaga, Hexapoda)

The morphology of the larval mandibular structures of the family Lycidae (Polyphaga) is characterized by facultative dicondyly, posterior articulation with long mandibular rods, lateral location of the anterior condyle and its articulation with a paired non‐cranial structure. It is compared to that of Eucrustacea, Chilopoda, Entognatha, Microcoryphia and Zygentoma and found to be more reminiscent of the Entognatha. The phylogenetic implications of this conclusion are discussed, with the Pterygota and Dicondylia hypothesized to be non‐monophyletic.     

Tikiguania and the antiquity of squamate reptiles (lizards and snakes)

Tikiguania estesi is widely accepted to be the earliest member of Squamata, the reptile group that includes lizards and snakes. It is based on a lower jaw from the Late Triassic of India, described as a primitive lizard related to agamids and chamaeleons. However, Tikiguania is almost indistinguishable from living agamids; a combined phylogenetic analysis of morphological and molecular data places it with draconines, a prominent component of the modern Asian herpetofauna. It is unlikely that living agamids have retained the Tikiguania morphotype unchanged for over 216 Myr; it is much more conceivable that Tikiguania is a Quaternary or Late Tertiary agamid that was preserved in sediments derived from the Triassic beds that have a broad superficial exposure. This removes the only fossil evidence for lizards in the Triassic. Studies that have employed Tikiguana for evolutionary, biogeographical and molecular dating inferences need to be reassessed.     

Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms

An important challenge in evolutionary biology is to understand how major changes in body form arise. The dramatic transition from a lizard-like to snake-like body form in squamate reptiles offers an exciting system for such research because this change is replicated dozens of times. Here, we use morphometric data for 258 species and a time-calibrated phylogeny to explore rates and patterns of body-form evolution across squamates. We also demonstrate how time-calibrated phylogenies may be used to make inferences about the time frame over which major morphological transitions occur. Using the morphometric data, we find that the transition from lizard-like to snake-like body form involves concerted evolution of limb reduction, digit loss, and body elongation. These correlations are similar across squamate clades, despite very different ecologies and >180 million years (My) of divergence. Using the time-calibrated phylogeny and ancestral reconstructions, we find that the dramatic transition between these body forms can occur in 20 My or less, but that seemingly intermediate morphologies can also persist for tens of millions of years. Finally, although loss of digits is common, we find statistically significant support for at least six examples of the re-evolution of lost digits in the forelimb and hind limb.     

The bony labyrinth of Platecarpus (Squamata: Mosasauria) and aquatic adaptations in squamate reptiles

Mosasaurs were among the last marine reptiles that lived before the Cretacesous–Paleogene extinction. Little is known about the sensory evolution of mosasaurs in relation to their aquatic lifestyle. In this study, the braincase of Platecarpus was CT-scanned and virtual models were constructed showing the bony labyrinth — or the inner ear — a sensory apparatus for balance and hearing. The virtual inner ear consists of the semicircular canals, vestibule, and cochlea. Compared with extant squamates, Platecarpus resembles sea snakes in having a small vestibule with a flat dorsal surface, but it differs from non-mosasaurian squamates in having rounded semicircular canals. Phylogenetic linear regression analysis supports a linear relationship, independent from phylogeny, between the length of the three semicircular canals and the length of the skull. The semicircular canals of Platecarpus are shorter than predicted, but the fossil data fell within the 95% prediction interval calculated from the extant data and the skull length of Platecarpus. Although size reduction of the bony labyrinth has been associated with aquatic adaptions in mammals, our results suggest that in squamates, semicircular canal size is related to skull size rather than habitat preference.     

Comparative histology of the vaginal–cloacal region in Squamata and its phylogenetic implications

We described the histology and morphology of the vaginal–cloacal region in 18 species from 12 Squamata families. This comparative study revealed a wide variation in the cloacal morphology. Fifteen morphological characters were considered to be primary homology hypotheses and were optimized over the topology derived from the parsimony analysis of the available soft morphological evidence, including the characters described in this study. The synapomorphies optimized for Squamata are bifid urodaeum, common urodaeal cavity with similar histological features of the urodaeal horns, and presence of glands in the anterior urodaeum; for Scleroglossa the synapomorphy is the lateral position of the vaginal intrusion into the anterior urodaeal chamber, for Nyctisaura + Scincomorpha the synapomorphy is the presence of a bifid posterior urodaeum; and for Xantusidae + Annulata it is the presence of simple glands in the anterior urodaeum. The central position of the vaginal intrusion into the urodaeal chamber and the intraepithelial position of the glandular unit in the anterior urodaeum behave as autapomorphies for Iguanidae. This study contributes evidence that defines the relationships within Scleroglossa. Cloacal features provide interesting information that is useful as a source of morphological characters for phylogenetic studies in Squamata.     

The skull of the Upper Cretaceous snake Dinilysia patagonica Smith‐Woodward, 1901, and its phylogenetic position revisited

The cranial anatomy of Dinilysia patagonica, a terrestrial snake from the Upper Cretaceous of Argentina, is redescribed and illustrated, based on high‐resolution X‐ray computed tomography and better preparations made on previously known specimens, including the holotype. Previously unreported characters reinforce the intriguing mosaic nature of the skull of Dinilysia, with a suite of plesiomorphic and apomorphic characters with respect to extant snakes. Newly recognized plesiomorphies are the absence of the medial vertical flange of the nasal, lateral position of the prefrontal, lizard‐like contact between vomer and palatine, floor of the recessus scalae tympani formed by the basioccipital, posterolateral corners of the basisphenoid strongly ventrolaterally projected, and absence of a medial parietal pillar separating the telencephalon and mesencephalon, amongst others. We also reinterpreted the structures forming the otic region of Dinilysia, confirming the presence of a crista circumfenestralis, which represents an important derived ophidian synapomorphy. Both plesiomorphic and apomorphic traits of Dinilysia are treated in detail and illustrated accordingly. Results of a phylogenetic analysis support a basal position of Dinilysia, as the sister‐taxon to all extant snakes. The fossil taxa Yurlunggur, Haasiophis, Eupodophis, Pachyrhachis, and Wonambi appear as derived snakes nested within the extant clade Alethinophidia, as stem‐taxa to the crown‐clade Macrostomata. The hypothesis of a sister‐group relationship between Dinilysia and Najash rionegrina, as suggested by some authors, is rejected by the results of our analysis. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 194–238.     

Pollen morphology of the Swertiinae (Gentianaceae): phylogenetic implications

Recent molecular surveys of the Swertiinae (Gentianaceae–Gentianeae) revealed unexpected phylogenetic relationships, including polyphyly of the genera Gentianella , Jaeschkea , Lomatogonium and Swertia . To find new non-molecular characters supporting the phylogeny, we examined the exine variation of 73 species of all major lineages of subtribe Swertiinae using environmental scanning electron miscroscopy supplementing older, mainly light microscopical, studies. In contrast to previous studies, we were able to pick out taxa from phylogenetic key positions with particular focus on Swertia . Many distantly related taxa such as parts of Frasera , Gentianopsis , Halenia , Gentianella , Megacodon and several lineages of Swertia share a striate–reticulate or reticulate exine pattern. This is interpreted as the plesiomorphic character state of Swertiinae. There is also considerable variation of derived patterns; for example, different types of microechinate or almost smooth pollen was repeatedly observed in distantly related groups. Another extreme was the ring-shaped reticulation found in a North American species of Gentianopsis . Unfortunately, major relationships as revealed by molecular analyses were rarely supported because of the abundance of the plesiomorphic type and homoplasy even on low taxonomic levels; for example, within Lomatogonium . Exine variation was particularly useful in characterizing independent lineages of Swertia . For example, according to pollen characters and in agreement with other data, the Asian Swertia cuneata is a sister group of a strongly diversified African lineage and Swertia yunnanensis , which is rather aberrant in flower morphology, seems close to parts of Lomatogonium .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 323–341.     

External morphology and phylogenetic significance of the dorsal/neck organ in the Conchostraca and the head pores of the cladoceran family Chydoridae (Crustacea, Branchiopoda)

On basis of a SEM study the homology between the neck/dorsal organ of the Conchostraca and the head pores of the cladoceran family Chydoridae is established. Species of Lynceus (Conchostraca) and Eurycercus (Chydorinae) show a characteristical similar arrangement of four elevated areas within a circular/oval organ. Presence of two lateral pores may be an apomorphy for the Chydoridae lost in the Chydorinae and in some other genera. Some species of the Chydoridae (Rhynchotalona falcta and Tretocephala ambigua) display what can be interpreted as intermediate stages between the circular/oval organs in Eurycerus and more aberrant neck organ structures in the remaining Chydoridae. A characteristic neck organ morphology — two widely separated median pores with two smaller pores in between and without lateral pores — is considered as a synapomopphy for the Chydorinae. In contrast, no component of the neck organ morphology could be given synapomorphic status for all the species of the Aloninae. A number of potential apomorphies, related to the neck organ, seem to place subgroups of the Aloninae closer to the Chydorinae than to the rest of the subfamily. These apomorphies include, among others, elongation of the neck organr after Eurycercus has been branched off and subdivision of the neck organ into discrete pores after Rhynchotalona and Tretocephala has been branched off. If this interpretation is correct it will leave the Aloninae paraphyletic with respect to the Chydorinae.     

Gross brain morphology of Hypoptopomatinae and Neoplecostominae (Siluriformes: Loricariidae): Comparative anatomy and phylogenetic implications

Hypoptopomatinae and Neoplecostominae include about 250 valid species, a substantial portion of loricariid catfishes. Although the relationships among the members of these subfamilies have been inferred by many authors, the most recent hypotheses based on morphological and molecular data differ widely. Herein, we provide new data on the morphology of the central nervous system, and evaluate the usefulness of these characters in phylogenetic inference. To accomplish this, we characterized the gross brain morphology of those catfishes, and analyzed 54 neuroanatomical characters in a total of 40 terminal taxa representing Hypoptopomatinae and Neoplecostominae, and also members of Delturinae and Hypostominae as outgroups. Hypoptopomatinae and Neoplecostominae are recovered as separate subfamilies, and most of our results are compatible with morphology‐based analyses. We conclude that neuroanatomy provides an informative source of new characters with strong phylogenetic signal at all recovered taxonomic levels.     

The ovaries of aphids (Hemiptera,Sternorrhyncha, Aphidoidea): morphology and phylogenetic implications

The ovaries of aphids belonging to the families Eriosomatidae, Anoeciidae, Drepanosiphidae, Thelaxidae, Aphididae, and Lachnidae were examined at the ultrastructural level. The ovaries of these aphids are composed of several telotrophic ovarioles. The individual ovariole is differentiated into a terminal filament, tropharium, vitellarium, and pedicel (ovariolar stalk). Terminal filaments of all ovarioles join together into the suspensory ligament, which attaches the ovary to the lobe of the fat body. The tropharium houses individual trophocytes and early previtellogenic oocytes termed arrested oocytes. Trophocytes are connected with the central part of the tropharium, the trophic core, by means of broad cytoplasmic processes. One or more oocytes develop in the vitellarium. Oocytes are surrounded by a single layer of follicular cells, which do not diversify into distinct subpopulations. The general organization of the ovaries in oviparous females is similar to that of the ovaries in viviparous females, but there are significant differences in their functioning: (1) in viviparous females, all ovarioles develop, whereas in oviparous females, some of them degenerate; (2) the number of germ cells per ovariole is usually greater in females of the oviparous generation than in females of viviparous generations; (3) in oviparous females, oocytes in the vitellarium develop through three stages (previtellogenesis, vitellogenesis, and choriogenesis), whereas in viviparous females, the development of oocytes stops after previtellogenesis; and (4) in the oocyte cytoplasm of oviparous females, lipid droplets and yolk granules accumulate, whereas in viviparous females, oocytes accrue only lipid droplets. Our results indicate that a large number of germ cells per ovariole represent the ancestral state within aphids. This trait may be helpful in inferring the phylogeny of Aphidoidea.     

First Neogene skulls of Doedicurinae (Xenarthra,Glyptodontidae): morphology and phylogenetic implications

Among Glyptodontidae, Doedicurinae (late Miocene–early Holocene) includes the glyptodonts with the largest size and latest records. Doedicurinae is mainly characterised by a smooth surface of the osteoderms with large foramina, and a particular morphology of the caudal tube. All taxa except one (Doedicurus clavicaudatus) have been recognised and characterised on the basis of remains of caudal tubes and/or dorsal carapaces. This situation produced an evident overestimation of the real diversity of this group, and a taxonomic revision is needed. In fact, no Neogene skulls were known. We present and describe the first two Neogene skulls belonging to Doedicurinae (cf. Eleutherocercus antiquus). The materials come from the El Polvorín and Chapadmalal Formations, in the surroundings of Olavarría and Mar del Plata localities, respectively (Buenos Aires province, Argentina). A cladistic analysis was carried out in order to situate these materials among Glyptodontidae and inferring new synapomorphies at skull level in Doedicurinae. Cf. Eleutherocercus antiquus clusters with the Pleistocene species Doedicurus clavicaudatus showing three unambiguous synapomorphies, which in turn represents the first skull synapomorphies for Doedicurinae. Finally, the presence of cf. Eleutherocercus antiquus in the El Polvorín and Chapadmalal Formations suggests that the stratigraphic distribution of this species could include the Montehermosan–Chapadmalalan interval.     

A new phylogenetic classification for the gymnophthalmid genera Cercosaura , Pantodactylus and Prionodactylus (Reptilia: Squamata)

Because of the poor state of knowledge of many of the gymnophthalmid genera, systematic revision is necessary to render the classification consistent with evolutionary history. To that end, I conducted a review of the species of three genera of the Cercosaurinae which appear to form a monophyletic group: Cercosaura , Pantodactylus , and Prionodactylus . Phylogenetic analysis of 61 morphological characters was conducted after specimens of all species were examined to evaluate the composition of each taxon. The phylogenetic reconstruction suggested that the genus Prionodactylus was paraphyletic. A new phylogenetic classification is proposed that synonymizes Pantodactylus and Prionodactylus with Cercosaura. Cercosaura is redefined to include 11 species and seven subspecies. A key is provided to distinguish among species.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 101−115.     

Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)

Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.     

The larval head morphology of Xyela sp. (Xyelidae, Hymenoptera) and its phylogenetic implications

Larval head structures of Xyela sp. are described in detail. The characters are compared to conditions found in larvae of other groups of Hymenoptera and Endopterygota. Like other symphytan larvae the immature stages of Xyelidae are mainly characterized by presumably plesiomorphic features of the head. The head sutures are well developed and all parts of the tentorium are present. The labrum is free and a complete set of labral muscles is present. The maxillae are in a retracted position. In contrast to other hymenopteran larvae Xyela possesses a clypeofrontal suture, a comparatively long antenna and three well‐developed antennal muscles. Apomorphic features of Xyela are the absence of muscles associated with the salivarium and the complete absence of Musculus craniocardinalis. A clade comprising Orussidae and Apocrita is supported by the unsegmented maxillary and labial palps and the absence of the lacinia. Six potential autapomorphies for the Hymenoptera were revealed: (1) the caudal tentorial apodeme, (2) the bifurcated tendon of Musculus craniomandibularus internus, (3) the lateral lobe of the cardo, (4) the origin of M. tentoriohypopharyngalis from the posterior head capsule, (5) the exceptionally strong prepharyngo‐pharyngeal longitudinal muscle and (6) the longitudinal muscle of the silk press. The maxillolabial complex, the vestigial M. craniocardinalis and a distinctly developed labio‐hypopharyngeal lobe bearing the opening of the salivary duct are potential synapomorphies of Hymenoptera and Mecopterida. The globular, orthognathous head capsule, the modified compound eyes, the occipital furrow and the X‐shaped tentorium are features with unclear polarity shared by Hymenoptera and Mecoptera.     

Ultrastructure of spermatozoa of orsolobidae (Haplogynae,Araneae) with implications on the evolution of sperm transfer forms in Dysderoidea

Haplogynae are highly diverse with respect to the primary male genital system and sperm characteristics. Additionally, all sperm transfer forms (STF) known for spiders are present. Besides individually transferred sperm (cleistospermia), sperm are transferred as conjugates, both primary (synspermia) and secondary sperm conjugates (coenospermia, rouleaux) occur. Nevertheless, the ultrastructure of spermatozoa and STF are described for few Haplogynae and often only one representative species was studied, resulting in a superficial insight in the evolution of these traits. To elucidate the evolution of STF within Haplogynae we investigated representatives of four genera of the dysderoid family Orsolobidae. Our data show the presence of synspermia (Orsolobus, Osornolobus, Hickmanolobus, and Tasmanoonops) and also cleistospermia (Osornolobus). The occurrence of different STF within one family or even genus has not been described for any other spider taxon so far. Moreover, the synspermia of species of Tasmanoonops and Hickmanolobus were not covered by a secretion sheath suggesting a previously unknown strategy of transferring sperm that is possibly related to sperm residency time or female triggered processes after copulation. Based on serial ultrathin sectioning and subsequent 3D‐reconstruction, we obtained detailed measurements revealing remarkable size differences of STF. To evaluate the previously suggested correlation with the most distal region of the spermophor inside the embolus (intromittent part of the copulatory organ) we measured the diameter of the spermophor using micro‐computed X‐ray tomography data to obtain corresponding morphometric parameters. Based on these data only two species show similarity in STF and spermophor diameter. J. Morphol. 275:1238–1257, 2014. © 2014 Wiley Periodicals, Inc.