Academic literature on the topic 'Lizards – Classification'

The Liolaemidae lizard evolutionary radiation has resulted from active spatial expansions into an extensive territorial area accompanied by active events of cladogenesis that have produced high levels of taxonomic and ecological diversity, especially within the Liolaemus genus. As a result, these lizards have been for decades the subject of intense taxonomic and systematic debates. Here, I provide an analysis of a recent paper where discussions on Liolaemidae diversity and classification involved biased and arbitrary interpretations and observations of two previously published monographs.

Although tropical forest birds are known to prey upon small lizards and frogs, no study has documented the attributes of vertebrate-eating birds or whether birds prey opportunistically on the different elements of the herpetofauna within tropical communities. This study is based on a 14-mo investigation on avian diet, supplemented with a 3-y census of frogs and a 1-y census of lizards in a humid forest of central Panama. From 91 bird species, 1086 regurgitates were collected, in which were found 75 lizards and 53 frogs. Over 50% of the common, primarily insectivorous bird species preyed upon lizards or frogs, with a mean frequency of 0.26 prey/sample. These birds (22 species, nine families) foraged on various substrates from different strata of the forest, fed on invertebrates averaging from 3.3 to 17.2 mm in length, weighed from 11 to 195 g, and had bill lengths that varied from 12.2 to 49.8 mm. Based on a logistic regression analysis, intensity of foraging at army-ant swarms was the variable that best explained the likelihood that a bird species preyed upon lizards, leading to a classification that was 91% correct. In contrast, bill length and body length classified correctly 88% of the frog-eating birds, which showed a fairly constant 1:7 bill length/body length ratio (as opposed to a mean but highly variable 1:10 ratio in other species). A multiple regression analysis showed that seasonal variation in intensity of lizard predation was positively related to arthropod abundance except during the breeding season when lizard intake decreased, presumably because nesting birds did not follow ant swarms. Intensity of frog predation correlated with frog abundance over time, the latter being inversely related to arthropod availability. Ninety-seven per cent of all lizards and frogs identified in the diet samples (n = 105) were from two genera, Anolis and Eleutherodactylus, respectively. Prey size distribution in the regurgitates suggested an optimal prey size of 33.5 mm snout-vent length (SVL) for lizards and 14.5 mm SVL for frogs. Birds preyed opportunistically on the different Anolis species, but almost exclusively upon juvenile individuals. Abundances of the different Eleutherodactylus species correlated with their predation rates, but these frogs represented only 10% of all the frogs observed during the censuses. The two most common local anurans, Colostethus flotator and Bufo typhonius, were not taken by any bird species.

Lizards of the family Diploglossidae occur in moist, tropical forests of Middle America, South America, and Caribbean islands. Our analyses based on new molecular and morphological data indicate that the widely distributed genera Celestus Gray, 1839 and Diploglossus Wiegmann, 1834 are paraphyletic. We restrict the former to Caribbean islands and the latter to South America and Caribbean islands. We assign species in Middle America, formerly placed in Celestus and Diploglossus, to Advenus gen. nov., Mesoamericus gen. nov., and Siderolamprus Cope, 1861. We assign species on Caribbean islands, formerly placed in Celestus, to Caribicus gen. nov., Comptus gen. nov., Celestus, Panolopus Cope, 1862, Sauresia Gray, 1852, and Wetmorena Cochran, 1927. Our phylogenetic tree supports three major clades in the family: Celestinae subfam. nov. (Advenus gen. nov., Caribicus gen. nov., Comptus gen. nov., Celestus, Panolopus, Sauresia, and Wetmorena), Diploglossinae (Diploglossus and Ophiodes Wagler, 1828), and Siderolamprinae subfam. nov. (Mesoamericus gen. nov. and Siderolamprus). Our timetree indicates that the diploglossid lineage originated in the early Cenozoic and established three major centers of diversification in the Americas: Middle America (siderolamprines and one celestine), South America (diploglossines), and Caribbean islands (celestines and diploglossines). The majority of threatened species are on Caribbean islands, with the major threats being deforestation and predation by the introduced mongoose. Molecular and morphological data indicate that there are many undescribed species in this family of lizards.

In this essay, we review concepts of taxonomic categories of anoles, reanalyze accumulated characteristics of these lizards,use these analyses to summarize the topology of the phylogenetic tree for anoles, and use consistent major branches ofthis topology to recommend a classification scheme for this large group of squamates. We then use this new taxonomy todraw inferences about the evolution of habitat use, as well as the geologic ages and geographic distribution of anolelineages. Our taxonomy eliminates problems of paraphyly inherent in previous classifications by elevating eight majorlineages to generic status (Anolis, Audantia, Chamaelinorops, Ctenonotus, Dactyloa, Deiroptyx, Norops, and Xiphosurus), providing diagnoses of those genera, and then doing the same for species groups within each genus. With the exceptionof 19 species, the contents of our generic categories are consistent with all recent phylogenetic reconstructions. Thus, therevised taxonomy appears to provide a stable classification for at least 95% of the 387 species currently recognized andincluded in our treatment of the group. We argue that these lizards originated in South America ~130 ma, where they werelarge in size and occupied niches focused on the canopy of rainforest trees. The radiation diverged into eight genera125–65 ma within a volcanic island arc that connected North and South America. This evolutionary diversificationgenerated three genera (Deiroptyx, Dactyloa, and Xiphosurus) that retained an ancestral large size and canopy niche focusand five genera (Anolis, Audantia, Chamaelinorops, Ctenonotus, and Norops) that became small, with niches focusedtoward the ground. The complicated divergence and accretion events that generated the current conformation of theAntillean islands, and eventually closed the Panamanian Portal, transported six island genera to their current centers ofdiversity (Anolis, Audantia, Chamaelinorops, Ctenonotus, Deiroptyx, and Xiphosurus), leaving two genera on themainland (Dactyloa and Norops). Our historical reconstruction makes Norops a much older radiation than previousreconstructions, allowing basal diversification of this species-rich lineage to occur on mainland terrains that eventuallyseparated from the mainland to become parts of Cuba and Jamaica. This early diversification extended into northern South America, where a basal lineage of Norops coevolved with Dactyloa prior to the mainland-island separation.

Synopsis The integrity of regional and local biological diversity is under siege as a result of multiple anthropogenic threats. The conversion of habitats, such as rain forests, into agricultural ecosystems, reduces the area available to support species populations. Rising temperatures and altered rainfall patterns lead to additional challenges for species. The ability of conservation biologists to ascertain the threats to a species requires data on changes in distribution, abundance, life history, and ecology. The International Union for the Conservation of Nature (IUCN) uses these data to appraise the extinction risk for a species. However, many species remain data deficient (DD) or unassessed. Here, I use 14 morphological traits related to locomotor function, habitat, and feeding to predict the threat status of over 400 species of lizards in the infraorder Iguania. Morphological traits are an ideal proxy for making inferences about a species’ risk of extinction. Patterns of morphological covariation have a known association with habitat use, foraging behavior, and physiological performance across multiple taxa. Results from phylogenetic general linear models revealed that limb lengths as well as head characters predicted extinction risk. In addition, I used an artificial neural network (ANN) technique to generate a classification function based on the morphological traits of species with an assigned IUCN threat status. The network approach identified eight morphological traits as predictors of extinction risk, which included head and limb characters. The best supported model had a classification accuracy of 87.4%. Moreover, the ANN model predicted >18% of DD/not assessed species were at risk of extinction. The predicted assessments were supported by other sources of threat status, for example, Convention on International Trade in Endangered Species appendices. Because of the functional link between morphology, performance, and ecology, an ecomorphological approach may be a useful tool for rapid assessment of DD or poorly known species.

We provide a critical review of a recent taxonomic revision of Chilean Liolaemus lizards (Iguania: Liolaemidae) by Pincheira-Donoso and Núñez (2005) and a recent paper (PincheiraDonoso et al. 2008), which proposed several new taxonomic and phylogenetic arrangements. We document fundamental problems with many of the proposed taxonomic revisions in both publications, which if followed, could lead to serious taxonomic confusion. In Pincheira-Donoso and Núñez (2005) a subgeneric classification is erected, which was produced by outdated methods (phenetic analyses), cannot be replicated (no matrix is presented), and is taxonomically untenable (some of the subgenera are nested within other subgenera). Most of the taxonomic groups that are proposed have been previously proposed, albeit differently constituted, yet often previous research is not given attribution; when findings are different, the research of others is either overlooked or dismissed without comment. The diagnoses of species and subspecies (including several newly proposed taxa) are often written in an authoritative manner (without supporting data or information), making them insufficient for distinguishing the focal taxon from others belonging to the same group, finally leading to uncertainty regarding the validity of several of the newly proposed taxa, combinations, or synonymies. We also describe less egregious errors of omission and commission. In Pincheira-Donoso et al. (2008), most of the proposals follow the Pincheira-Donoso and Núñez (2005) revisions, some species are allocated to groups without consistent cladistic support and other proposed relationships are based on incomplete evidence from other studies dismissing the limitations of the arrangement. Critical species are not identified in a list of material examined. Finally, Pincheira-Donoso et al. (2008) present a somewhat outdated and biased discussion of the relative value of using molecules or morphology in systematics. In light of these limitations, and in an effort to stabilize and prevent further taxonomic confusion, we provide an updated phylogenetic classification of the currently recognized lizards of the family Liolaemidae (Ctenoblepharys, Liolaemus, and Phymaturus), which is based on a consensus of studies published since the first phylogenetic major revision of the clade in 1995.

An individual's sex depends upon its genes (genotypic sex determination or GSD) in birds and mammals, but reptiles are more complex: some species have GSD whereas in others, nest temperatures determine offspring sex (temperature-dependent sex determination). Previous studies suggested that montane scincid lizards ( Bassiana duperreyi , Scincidae) possess both of these systems simultaneously: offspring sex is determined by heteromorphic sex chromosomes (XX–XY system) in most natural nests, but sex ratio shifts suggest that temperatures override chromosomal sex in cool nests to generate phenotypically male offspring even from XX eggs. We now provide direct evidence that incubation temperatures can sex-reverse genotypically female offspring, using a DNA sex marker. Application of exogenous hormone to eggs also can sex-reverse offspring (oestradiol application produces XY as well as XX females). In conjunction with recent work on a distantly related lizard taxon, our study challenges the notion of a fundamental dichotomy between genetic and thermally determined sex determination, and hence the validity of current classification schemes for sex-determining systems in reptiles.

AbstractWe investigated life history characters of the Cape grass lizard, Cordylus anguinus, and relate them to survival in the fire-prone habitat in which it occurs. Unlike in other cordylids, reproductive activity was found to be asynchronous among females, with vitellogenic and gravid females encountered virtually throughout the year. Aseasonal breeding will circumvent reduction or complete loss of reproductive effort for any given year due to fire. Female grass-lizards attain significantly larger body sizes than males. Clutch size ranged from three to seventeen and was positively correlated with snout-vent length. Maximum clutch size is more than three times that recorded for any other cordylid. We suggest that high fecundity will allow quick recruitment after a fire. To determine the reproductive cycle exhibited by males, testicular volume and seminiferous tubule diameter were measured, and spermatogenic activity assessed qualitatively, using Licht's classification system. Our data indicate that C. anguinus has a post-nuptial spermatogenic cycle. The species differs from other cordylids having a post-nuptial cycle, in that spermatogenesis already commences in spring.

The transition between terrestrial varanoid lizards and aquatic mosasaurs through the intermediate, semi-aquatic aigialosaurs is fully documented. Aigialosaurs are shown to possess a mosaic of mosasaurian (configuration of the skull, jaw and tail) and terrestrial varanoid characters (appendicular skeleton and trunk).
The taxonomic position of the Aigialosauridae within the superfamily Varanoidea is evaluated. Based on character states previously used to define the Varanoidea, neither the specific affinities of aigialosaurs nor the sister-group relationships of earlier members of the terrestrial varanoid assemblage can be securely established. For this reason, the specific character states involved have been reexamined and alternative hypotheses of relationship have been considered.

BACKGROUND:The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata.RESULTS:The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.CONCLUSIONS:We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.

Dissertation (PhD)--University of Stellenbosch, 2007.
ENGLISH ABSTRACT: The taxonomic status of southern Africa’s rupicolous crag lizards (genus Pseudocordylus) was investigated. As considerable confusion exists in the literature regarding the type specimens and type localities of the various taxa, resolution of these problems were considered the starting point of the study. Examination of museum specimens allowed for the designation of lectotypes, alloparalectotypes and/or paralectotypes. Of particular relevance to this study was the rediscovery of Andrew Smith’s type specimens of P. m. melanotus and P. m. subviridis. Restriction of the type locality of P. m. subviridis, based on entries in Smith’s diary and journal, allowed for the confirmation of previous interpretations and definitions of the two taxa. The geographical distribution of the various taxa and populations was determined using an extensive locality database. Two kinds of molecular markers, namely allozymes and mitochondrial DNA, were used in an attempt to resolve taxon boundaries within the P. melanotus species complex. The allozyme analysis indicated that P. m. melanotus might be polyphyletic and comprised of two unrelated lineages. Furthermore, fixed allelic differences between parapatric populations of P. m. melanotus and P. m. subviridis, and between sympatric populations of P. m. subviridis and P. langi, suggested that all three forms might be considered full species, with the possibility of more cryptic species present in the complex. Pseudocordylus transvaalensis differed from most other populations by 1-3 fixed allelic differences, but was indistinguishable from the Nkandhla district (central KwaZulu-Natal) population of P. m. melanotus. There were no heterozygous individuals in a sample from Monontsha Pass (Qwa-Qwa), a population reportedly comprising P. m. melanotus and P. m. subviridis, as well as intermediates, and all specimens were assignable to P. m. subviridis. The allozyme study was, however, based on phenetic principles and for further taxonomic resolution a cladistic approach was required. An mtDNA analysis (16S rRNA gene) using Maximum Parsimony, Maximum Likelihood and Bayesian analyses was therefore conducted to determine phylogenetic relationships among species and subspecies and to re-assess the taxonomic status of forms in the P. melanotus species complex. The mtDNA analysis corroborated most of the results obtained in the allozyme analysis. Firstly, P. langi was again found to be basal. With the addition of P. microlepidotus and P. spinosus to the ingroup, it is now apparent that P. langi is the basal species in the genus. (Recent studies have indicated that P. capensis and P. nebulosus are not congeneric with Pseudocordylus.) Secondly, the 16S rRNA results confirm that P. m. melanotus, as presently construed, is comprised of two clades that are not sister groups. The northern populations of P. m. melanotus (Sabie and Lochiel) form a fairly deeply divergent clade that may represent a separate species. The Nkandla population was, however, found to cluster with the other southern P. m. melanotus populations and not with P. transvaalensis as was the case in the allozyme electrophoretic analysis. However, the most surprising result of the 16S rRNA analysis was the finding that both P. microlepidotus and P. spinosus are embedded within P. m. subviridis. This suggests that these two species evolved from within P. m. subviridis and may have been separated only recently, with rapid morphological divergence occurring, but with limited genetic differentiation. It is suggested that all of the above three taxa be provisionally treated as full species. There was also morphological support for the uniqueness of all groupings indicated by the mtDNA analysis. Pseudocordylus transvaalensis is characterized by its large size, unique dorsal and gular (black) colour patterns, as many as three horizontal rows of lateral temporal scales, a series of small scales posterior to the interparietal scale, and usually two subocular scales behind the median subocular on either side of the head. The various populations currently classified under the name P. melanotus are more difficult to separate, but P. m. melanotus and P. m. subviridis usually differ as follows: frontonasal divided in P. m. melanotus, undivided in P. m. subviridis (and most Northern melanotus); lateral temporals in two rows, upper more elongate versus single row of much elongated scales; longitudinal rows of dorsolaterals closely-set versus widely separated; femoral pores of females pit-like versus deep with secretory plug. Northern melanotus differs from Southern melanotus in usually having an undivided frontonasal scale and seldom having a small scale present behind the frontonasal. Pseudocordylus langi has unique dorsal and gular colour patterns (including a series of blue spots on the flanks), granular dorsals with 6-9 paravertebral rows of enlarged flat scales, high total numbers of femoral pores (25-34) and usually only five (smooth not keeled or ridged) infralabial scales on either side of the head. Pseudocordylus spinosus also has unique dorsal and gular colour patterns, spinose lateral scales, frontonasal longer than wide and excluded from the loreal scales, low total femoral pore counts (6-9), and females (not only males) have differentiated femoral scales. Both Principal Components Analysis (PCA) and Canonical Discriminant Analysis (CDA) distinguished four groups, namely P. transvaalensis, P. langi, P. spinosus and a P. melanotus/subviridis/microlepidotus cluster. A separate CDA of all P. melanotus populations partly distinguished between Southern melanotus and P. m. subviridis, and largely separated Northern melanotus; whereas a CDA of P. transvaalensis showed that all three allopatric populations are 100% distinguishable in morphological space. A Nested Clade Analysis indicated that fragmentation as well as range expansion played a role in the distribution of the P. melanotus species complex. This may be explained by climatic oscillations (high-low temperatures and wet-dry cycles) during the Cenozoic that caused habitat expansion and contraction. Based on the topology of the mtDNA phylogram it is apparent that the genus Pseudocordylus originated along the eastern escarpment. A P. langi-like ancestor may have had an extensive range along the eastern escarpment, with the Maloti-Drakensberg forming the southern limit of its range. During a subsequent rise in global temperatures, range contraction and fragmentation took place, leaving an isolated population in the south and one in the north. The southern population survived unchanged in the Maloti-Drakensberg refugium, but the northern population was forced to adapt to the warmer conditions. Thereafter, the northern form expanded its range again, but during a subsequent cooler period, range contraction occurred, resulting in an isolated north-eastern population in the Sabie-Lochiel area in Mpumulanga (Northern melanotus) and a western population. Relationships in the latter clade are not sufficiently resolved to allow further reconstruction of biogeographic history, but it is clear that a P. m. subviridis-like form became isolated in the south where it eventually came into contact with P. langi at high elevations. Pseudocordylus m. subviridis eventually extended its range southwestwards into the inland mountains of the Eastern Cape and Cape Fold Mountains to give rise to the P. microlepidotus complex. This cycle of range expansion and contraction may also account for the isolated populations at Suikerbosrand, Nkandhla district, and in the Amatole-Great Winterberg mountain region. Furthermore, it is suggested that P. spinosus originated from a P. m. subviridis-like ancestral population that became isolated on the lower slopes of the Drakensberg where terrestrial predation pressure resulted in a quick shift in morphology from fairly smooth body scales to a more spiny morphology.
AFRIKAANSE OPSOMMING: Die taksonomiese status van suidelike Afrika se rotsbewonende krans-akkedisse (genus Pseudocordylus) is ondersoek. Omdat daar aansienlike verwarring in die literatuur bestaan met betrekking tot die tipe monsters en die tipe lokaliteite van die verskillende taksa, is die oplossing van hierdie probleme as die beginpunt van hierdie studie geneem. Die bestudering van akkedismonsters in museums het dit moontlik gemaak om lektotipes, alloparalektotipes en/of paralektotipes aan te wys. Van besondere belang vir hierdie studie is die herontdekking van Andrew Smith se tipe monsters van P. m. melanotus en P. m. subviridis. Die beperking van die tipe lokaliteit van P. m. subviridis, gebaseer op inskrywings in Smith se dagboek en joernaal, het dit moontlik gemaak om vorige interpretasies en definisies van die twee taksa te bevestig. Die geografiese verspreiding van die verskillende taksa en bevolkings is bepaal deur middel van ’n omvattende lokaliteit databasis. Twee soorte molekulêre merkers, naamlik allosieme en mitokondriale DNS, is gebruik in ʼn poging om uitsluitsel te verkry oor die takson-grense binne die P. melanotus-spesiekompleks. Die allosiem-analise het daarop gedui dat P. m. melanotus moontlik polifileties mag wees en uit twee onverwante stamboom-vertakkings kan bestaan. Verder het vaste alleliese verskille tussen parapatriese bevolkings van P. m. melanotus en P. m. subviridis, en tussen simpatriese bevolkings van P. m. subviridis en P. langi, daarop gedui dat al drie vorme as volledige spesies beskou kan word, met die moontlikheid dat meer kriptiese spesies in die kompleks teenwoordig kan wees. Pseudocordylus transvaalensis het van die meeste ander bevolkings verskil met 1-3 vaste alleliese verskille, maar was ononderskeibaar van die bevolking van P. m. melanotus van die Nkandhla distrik (sentraal KwaZulu-Natal). Daar was slegs homosigote individue in ʼn steekproef van Monontsha Pas (Qwa-Qwa), ʼn bevolking wat volgens die literatuur P. m. melanotus en P. m. subviridis, sowel as intermediêre omvat, en alle monsters was toekenbaar aan P. m. subviridis. Die allosiemstudie is egter gebaseer op fenetiese beginsels en vir verdere taksonomiese oplossing is ʼn kladistiese benadering vereis. ʼn Mitokondriale DNS-analise (16S rRNS geen) wat gebruik maak van Maksimum Parsimonie-, Maksimum Waarskynlikheids- en Bayes-analises is daarom uitgevoer om die filogenetiese verwantskappe tussen spesies en subspesies te bepaal en om die taksonomiese status van vorme in die P. melanotus-spesiekompleks te herondersoek. Die mtDNS-analise het die meeste van die resultate van die allosiem-analise bevestig. Eerstens, P. langi is weer bevind om basaal te wees. Met die byvoeging van P. microlepidotus en P. spinosus tot die binne-groep het dit nou duidelik geword dat P. langi die basale spesie in die genus is. (Onlangse studies het aangedui dat P. capensis en P. nebulosus nie kongeneries met Pseudocordylus is nie.) Tweedens, die 16S rRNS resultate bevestig dat P. m. melanotus, soos tans vasgestel, saamgestel is uit twee klade wat nie sustergroepe is nie. Die noordelike bevolkings van P. m. melanotus (Sabie en Lochiel) vorm ʼn redelik diep divergente klaad wat ʼn afsonderlike spesie mag verteenwoordig. Dit is egter bevind dat die Nkandla bevolking saamgegroepeer het met die ander suidelike P. m. melanotus-bevolkings en nie met P. transvaalensis soos wat die geval was in die allosiem-elektroforetiese analise nie. Die mees verbasende resultaat van die 16S rRNS-analise was egter die bevinding dat beide P. microlepidotus en P. spinosus genestel was binne P. m. subviridis. Dit dui daarop dat hierdie twee spesies kon ontwikkel het vanuit P. m. subviridis en slegs onlangs van mekaar geskei het, toe vinnige morfologiese splitsing voorgekom het, maar met beperkte genetiese differensiasie. Dit word voorgestel dat al drie die bogenoemde taksa voorlopig as volledige spesies beskou word. Daar was ook morfologiese steun vir die uniekheid van al die groeperings wat die mtDNS-analise uitgewys het. Pseudocordylus transvaalensis kan uitgeken word aan sy bogemiddelde grootte, unieke dorsale en (swart) kleurpatrone op die keel, so veel as drie horisontale rye lateraaltemporale skubbe, ʼn reeks klein skubbe agter die interpariëtale skub, en gewoonlik twee subokulêre skubbe agter die middelste subokulêre skub op beide kante van die kop. Die verskillende bevolkings wat tans geklassifiseer word as P. melanotus is moeiliker om van mekaar te skei, maar P. m. melanotus en P. m. subviridis verskil gewoonlik soos volg: frontonasale skub in twee gedeel in P. m. melanotus, heel in P. m. subviridis (en in die meeste Noordelike melanotus); lateraal-temporale skubbe in twee rye, die boonste ry met verlengde skubbe teenoor ʼn enkele ry verlengde skubbe; longitudinale rye van dorsolaterale skubbe naby aan mekaar teenoor ver uit mekaar; femorale porieë van wyfies klein en vlak teenoor diep met sekreterende proppe. Noordelike melanotus verskil van Suidelike melanotus deurdat hulle gewoonlik ʼn heel frontonasale skub het en daar selde ʼn klein skub teenwoordig is agter die frontonasale skub. Pseudocordylus langi het unieke dorsale en keel-kleurpatrone (wat ʼn reeks blou kolle op die sye insluit), granulêre dorsale skubbe met 6-9 rye vergrote plat skubbe langs die rugsteen, ʼn groot totale aantal femorale porieë (25-34), en gewoonlik net vyf (glad, ongerif) infralabiale skubbe op elke kant van die kop. Pseudocordylus spinosus het ook unieke dorsale en keel-kleurpatrone, skerp laterale skubbe, frontonasale skub langer as wyd en nie in kontak met die loreale skubbe nie, klein totale aantal femorale porieë (6-9), en wyfies (nie net mannetjies nie) het gedifferensieerde femorale skubbe. Die Hoof-komponent Analise (HKA) en die Kanonieke Diskriminant Analise (KDA) het albei vier groepe geïdentifiseer, naamlik P. transvaalensis, P. langi, P. spinosus en ʼn P. melanotus/subviridis/microlepidotus groepering. ʼn Aparte KDA van alle P. melanotus bevolkings het gedeeltelik onderskei tussen Suidelike melanotus en P. m. subviridis, en die Noordelike melanotus is grootliks van die ander onderskei; terwyl ʼn KDA van P. transvaalensis daarop gedui het dat al drie allopatriese bevolkings 100% onderskeibaar in morfologiese ruimte is. ʼn Genestelde Klaad-Analise het aangedui dat fragmentasie, sowel as gebiedsuitbreiding, ʼn rol gespeel het in die verspreiding van die P. melanotus-spesiekompleks. Dit kan moontlik verklaar word deur die klimaatswisselinge (hoë-lae temperature en nat-droë siklusse) gedurende die Senosoikum wat habitat-uitbreiding en –verkleining veroorsaak het. Gebaseer op die topologie van die mtDNS filogram is dit duidelik dat die genus Pseudocordylus al langs die oostelike platorand ontstaan het. ʼn Voorouer soortgelyk aan P. langi kon ʼn uitgebreide gebied al langs die oostelike platorand gehad het, met die Maloti-Drakensberg wat die suidelike limiet van hierdie gebied gevorm het. Gedurende ʼn daaropvolgende toename in globale temperature het gebiedsverkleining en fragmentasie plaasgevind, wat ʼn geïsoleerde bevolking in die suide en een in die noorde tot gevolg gehad het. Die suidelike bevolking het onveranderd oorleef in die Maloti-Drakensberg skuilplek (“refugium”), maar die noordelike bevolking is geforseer om aan te pas in die warmer toestande. Daarna het die noordelike vorm se gebied weer uitgebrei, maar gedurende ʼn daaropvolgende koeler periode het gebiedsverkleining weer plaasgevind, met die gevolg dat daar ʼn geïsoleerde noord-oostelike bevolking in die Sabie-Lochiel-area in Mpumalanga (Noordelike melanotus) en ʼn bevolking in die weste was. Verwantskappe in die laasgenoemde klaad is nie voldoende opgelos om verdere rekonstruksie van die biogeografiese geskiedenis moontlik te maak nie, maar dit is duidelik dat ʼn vorm soortgelyk aan P. m. subviridis geïsoleer geraak het in die suide waar dit eindelik op hoë liggings in kontak gekom het met P. langi. Die gebied van P. m. subviridis is ook later suidweswaarts uitgebrei tot in die binnelandse berge van die Oos-Kaap en Kaapse Plooiberge om tot die ontstaan van die P. microlepidotuskompleks aanleiding te gee. Hierdie siklus van gebiedsuitbreiding en verkleining kan ook ʼn verklaring bied vir die geïsoleerde bevolkings by Suikerbosrand, Nkandhla distrik, en in die Amatole-Groot Winterberg-streek. Verder word voorgestel dat P. spinosus ontstaan het uit ʼn voorouerlike bevolking soortgelyk aan P. m. subviridis wat geïsoleerd geraak het op die laer hange van die Drakensberg waar die druk van aardsbewonende roofdiere tot ʼn vinnige verandering in morfologie vanaf redelik gladde liggaamskubbe tot ʼn meer skerppuntige morfologie gelei het.

In this thesis, I investigate the phylogeny and evolution of Lerista, a clade of more than 75 species of scincid lizards, distributed in arid, semi-arid, and seasonally dry habitats throughout Australia. Among extant tetrapods, Lerista is exceptional in comprising a large number of closely-related species displaying prodigious variability of body form; several species possessing well-developed, pentadactyl limbs resemble typical non-fossorial scincids in body proportions, while many other species exhibit varying degrees of limb reduction and body elongation, including two that are highly elongate and entirely limbless. The extensive variation in limb morphology observed among species, incorporating at least 20 distinct phalangeal configurations, has prompted some authors to identify Lerista as the best available model for studying limb reduction in squamates. Nonetheless, lack of a well-resolved phylogeny has impeded investigation of the pattern and mode of limb reduction and loss within the clade. The primary goal of my research was to furnish a comprehensive phylogenetic hypothesis for Lerista, enabling more sophisticated study of the evolution of limb morphology and body form in this clade than has previously been possible. A recent phylogenetic analysis of mitochondrial DNA sequences for a series of Australian Sphenomorphus group scincids (including two species of Lerista) recovered several well-supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage-level polytomies, I use ATP synthetase-β subunit intron sequences and the existing mitochondrial DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mitochondrial DNA and intron sequence data reveal a number of congruent clades, however, the relationships among these clades indicated by the two data sets are generally incongruent. Although this may be partly ascribed in to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mitochondrial DNA and intron fragments considered, if not essentially simultaneous. The pattern and rate of limb reduction in Lerista are investigated, employing a nearly complete phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes. Ancestral digit configurations reconstructed assuming this phylogeny indicate at least ten independent reductions in the number of digits from a pentadactyl condition, including four independent losses of all digits, three from pentadactyl or tetradactyl conditions. At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within no more than 3.6 million years. Patterns of digit loss for the manus and pes are consistent with selection for preserving hindlimb utility as the limbs are reduced, and suggest that intermediate digit configurations exhibited by extant species do not represent transitory stages in a continuing process of limb reduction. An increase in the relative length of the body is demonstrated to precede digit loss in lineages experiencing substantial reduction of the limbs, supporting the hypothesis that limb reduction and loss is a consequence of the adoption of lateral undulation as a significant locomotory mode. However, less extensive limb reduction may proceed in the absence of body elongation, perhaps due to a decrease in absolute body size. The exceptionally high frequency and rate of limb reduction in Lerista emphasise the potential for rapid and dramatic evolutionary transformation of body form in squamates. The substantial divergence of relative limb and body length evident within Lerista is more readily explained by the correlated progression model of phenotypic transformation than the independent blocks model. At each step in the attainment of a limb-reduced, elongate body form, alterations to the relative length of the limbs are accompanied by changes in relative snout-vent length (or vice versa) enabling the maintenance of locomotory ability. Nonetheless, some dissociation of hindlimb reduction and body elongation is possible, emphasising the potentially variable intensity of functional constraints and, accordingly, that the independent blocks model and correlated progression are extremes of a continuum of models (each invoking a different degree of functional integration) and do not describe discrete categories of phenotypic change. An increase in the extent of seasonally dry and arid habitats coincident with the origination of Lerista would have facilitated limb reduction and body elongation by furnishing an environment conducive to the adoption of fossorial habits, however, trends toward a limbless, highly elongate body form may be attributed primarily to the very low probability of re-elaborating reduced limbs. Such asymmetry in the probabilities of possible phenotypic changes may be a significant cause of evolutionary trends resulting in the emergence of higher taxa.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

In this thesis, I investigate the phylogeny and evolution of Lerista, a clade of more than 75 species of scincid lizards, distributed in arid, semi-arid, and seasonally dry habitats throughout Australia. Among extant tetrapods, Lerista is exceptional in comprising a large number of closely-related species displaying prodigious variability of body form; several species possessing well-developed, pentadactyl limbs resemble typical non-fossorial scincids in body proportions, while many other species exhibit varying degrees of limb reduction and body elongation, including two that are highly elongate and entirely limbless. The extensive variation in limb morphology observed among species, incorporating at least 20 distinct phalangeal configurations, has prompted some authors to identify Lerista as the best available model for studying limb reduction in squamates. Nonetheless, lack of a well-resolved phylogeny has impeded investigation of the pattern and mode of limb reduction and loss within the clade. The primary goal of my research was to furnish a comprehensive phylogenetic hypothesis for Lerista, enabling more sophisticated study of the evolution of limb morphology and body form in this clade than has previously been possible. A recent phylogenetic analysis of mitochondrial DNA sequences for a series of Australian Sphenomorphus group scincids (including two species of Lerista) recovered several well-supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage-level polytomies, I use ATP synthetase-β subunit intron sequences and the existing mitochondrial DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mitochondrial DNA and intron sequence data reveal a number of congruent clades, however, the relationships among these clades indicated by the two data sets are generally incongruent. Although this may be partly ascribed in to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mitochondrial DNA and intron fragments considered, if not essentially simultaneous. The pattern and rate of limb reduction in Lerista are investigated, employing a nearly complete phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes. Ancestral digit configurations reconstructed assuming this phylogeny indicate at least ten independent reductions in the number of digits from a pentadactyl condition, including four independent losses of all digits, three from pentadactyl or tetradactyl conditions. At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within no more than 3.6 million years. Patterns of digit loss for the manus and pes are consistent with selection for preserving hindlimb utility as the limbs are reduced, and suggest that intermediate digit configurations exhibited by extant species do not represent transitory stages in a continuing process of limb reduction. An increase in the relative length of the body is demonstrated to precede digit loss in lineages experiencing substantial reduction of the limbs, supporting the hypothesis that limb reduction and loss is a consequence of the adoption of lateral undulation as a significant locomotory mode. However, less extensive limb reduction may proceed in the absence of body elongation, perhaps due to a decrease in absolute body size. The exceptionally high frequency and rate of limb reduction in Lerista emphasise the potential for rapid and dramatic evolutionary transformation of body form in squamates. The substantial divergence of relative limb and body length evident within Lerista is more readily explained by the correlated progression model of phenotypic transformation than the independent blocks model. At each step in the attainment of a limb-reduced, elongate body form, alterations to the relative length of the limbs are accompanied by changes in relative snout-vent length (or vice versa) enabling the maintenance of locomotory ability. Nonetheless, some dissociation of hindlimb reduction and body elongation is possible, emphasising the potentially variable intensity of functional constraints and, accordingly, that the independent blocks model and correlated progression are extremes of a continuum of models (each invoking a different degree of functional integration) and do not describe discrete categories of phenotypic change. An increase in the extent of seasonally dry and arid habitats coincident with the origination of Lerista would have facilitated limb reduction and body elongation by furnishing an environment conducive to the adoption of fossorial habits, however, trends toward a limbless, highly elongate body form may be attributed primarily to the very low probability of re-elaborating reduced limbs. Such asymmetry in the probabilities of possible phenotypic changes may be a significant cause of evolutionary trends resulting in the emergence of higher taxa.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

South Africa is well known for its many, important fossil bearing deposits of Plio-Pleistocene age. Many of these sites contain abundant remains of extinct and extant animals including hominins. Non-herpetological fauna have been used to reconstruct important information about past environments and for chronological data. This study tried a different method; using herpefauna to establish past environments of Cooper’s Cave. Herpetological fauna potentially have numerous advantages in their use for such questions, including typically limited ranging behaviors, and specific temperature requirements. Despite these advantages only a few studies have even mentioned the presence of squamate fauna in the fossil assemblages of these sites. This study has demonstrated that herpefauna exists, in reasonable levels of abundance and with adequate preservation within the fossil record of the dolomitic region now known as the Cradle of Humankind. It has also demonstrated for the first time the presence of a relative abundance of herpefauna at numbers far greater than any previous study has recognized. The present study was however, handicapped in not being able to fully utilize the material at hand to interpret past environments, owing to the lack of comparative material needed to move beyond the family or generic level in most cases with any degree of confidence. However, Agamids and Pseudocordylids were described to generic level. However, the many shortcomings that this work highlighted should not be seen as reason not to pursue the study of herpefauna, but to improve present comparative collections and collecting methods around the fossils themselves.