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Systematics and phylogeography of the widely distributed African skink Trachylepis varia species complex
Abstract
A systematic study of the Trachylepis varia complex was conducted using mitochondrial and nuclear DNA markers for individuals sampled across the species range. The taxonomic history of T. varia has been complicated and its broad geographic distribution and considerable phenotypic variation has made taxonomic revision difficult, leading earlier taxonomists to suggest that T. varia is a species complex. We used maximum likelihood and Bayesian inference to estimate gene trees and a multilocus time-tree, respectively, and we used these trees to identify the major clades (putative species) within T. varia. Additionally, we used morphological and color pattern data to distinguish and revise the taxonomy of the southern African clades. The major clades recovered in the multilocus time-tree were recovered in each of gene trees, although the relationships among these major clades differed across gene trees. Genetic data support the existence of at least eight species within the T.varia complex, each of which originated during the mid to late Miocene or early Pliocene. We focus our systematic discussion on the southern African members of the T. varia complex, revive Trachylepis damarana (Peters, 1870) and T. laevigata (Peters, 1869), and designate lectotypes for T.damarana and T. varia.
Supplementary resources (3)
... Three species occur in northern South Africa, all of which are partly or entirely sympatric ( Figure 2) and are difficult to distinguish morphologically (Supplemental Material Table S2). Trachylepis damarana (Peters, 1870) and T. varia (Peters, 1867) can be identified by the length of the ventral and anterior margin of the second loreal scale, and T. laevigata (Peters, 1869) is differentiated from others by black longitudinal stripes on the dorsum that begin a few scale rows behind the nuchal scales (Weinell and Bauer 2018). Phylogenetic analyses have resulted in T. damarana and T. laevigata being raised to full species from synonymy with T. varia, but there are still a number of distinct lineages in the complex that are undescribed and currently assigned to T. cf. ...
... varia (Weinell and Bauer 2018). Although it is clear that the taxa in these two species complexes are genetically distinct at the species level (Weinell and Bauer 2018;Weinell et al. 2019), these analyses did not include individuals from areas of sympatry. Consequently, there is uncertainty as to the identification of individuals from these areas, as well as the geographic extent of sympatry. ...
... Initial identifications of new material from recent field surveys were made by examining morphological features with reference to commonly used field guides and literature (FitzSimons 1943;Branch 1998;Broadley 2000;Weinell and Bauer 2018;Supplementary Material Tables S1 and S2). For existing banked and GenBank material, we were unable to verify how each skink individual was initially identified, but we presume the collectors used these same standard literature sources and relevant diagnostic traits. ...
It is commonly recognised that natural history datasets contain locality errors that can compromise the utility of those datasets. However, another source of error in these datasets is taxonomic misidentifications, and this type of error is potentially common, particularly with regards to morphologically conservative species. For example, in the African skinks, the Trachylepis striata and T. varia species complexes each contain morphologically similar species that are commonly confused, despite being genetically distinct. Some species also are partly sympatric, and misidentifications are likely to be especially problematic in those areas. Using DNA barcoding, we assessed misidentification rates between species and applied the updated identifications to known distribution maps to examine whether those maps are accurate representations. Existing banked samples and newly collected samples were DNA barcoded using the mitochondrial 16S gene and supplemented with GenBank data. Identifications were made by matching sequences using haplotype networks that included material from near type localities. The barcode-based identifications were compared with the original identifications recorded for those samples. Taxonomic error was common, particularly in areas of presumed sympatry (error for T. striata species complex: 28%; T. varia species complex: 31%) and this resulted in inaccurately represented species distributions and areas of sympatry. Areas of sympatry were, however, confirmed for T. spilogaster/T. punctatissima, T. striata/T. punctatissima and T. damarana/T. laevigata/T. varia. Our findings corroborate other studies that demonstrate taxonomic error in existing datasets is a significant, but typically unrecognised problem, particularly for morphologically conservative species. This has implications for the utility of historical collections, citizen science records and public databases used in the formulation of species distribution maps, but also for other downstream analyses that rely on these datasets.
... For Ethiopia, the following nine species of Trachylepis have been recorded: Trachylepis brevicollis (Wiegmann, 1837), T. hildebrandtii (Peters, 1874), T. maculilabris (Gray, 1845), T. megalura (Peters, 1878), T. planifrons (Peters, 1878), T. quinquetaeniata (Lichtenstein, 1823), T. striata (Peters, 1844), T. varia (Peters, 1867) and T. wingati (Werner, 1908) (Largen & Spawls, 2006, 2010Sindaco et al., 2012). Although synonymized with T. varia by Loveridge (1923) the status and distinctness of T. isselii (Peters, 1871) from the Horn of Africa is still uncertain (Largen & Spawls, 2010;Sindaco et al., 2012;Weinell & Bauer, 2018). ...
... Both morphological and phylogenetic studies of Trachylepis indicate that numerous taxa with a broad distribution range represent several so far undetected species or even species complexes (Sindaco et al., 2012;Weinell & Bauer, 2018;Weinell et al., 2019). ...
... Characters for the morphological analyses were partially selected and modified based on previous taxonomic studies of Trachylepis (Weinell & Bauer, 2018;Marques et al., 2019) (Table 1). ...
Ethiopia is known for its highly endemic and rich herpetofaunal diversity shaped by its biogeographical patterns. Here, a new species of skink, Trachylepis boehmei sp. nov., is described from the Ethiopian Highlands. It differs from its congeners in having smooth uncarinated dorsal scales, 26-29 scale rows around midbody, a slender body of small size, a relatively short tail, a low eye-snout distance and a unique colour pattern with 6-8 darkish brown dorsal stripes. Based on morphological characteristics, its biogeographical pattern and comparisons with other similar congeners this new species is closely related to Trachylepis megalura. A published new record of Trachylepis wingati for the Kafa region is reexamined and identified as T. megalura. An updated comprehensive key to the Trachylepis found in Ethiopia is provided. In the context of ongoing phylogenetic and taxonomic revisions of Trachylepis and its species complexes the presence of further cryptic taxa can be expected also for the Ethiopian biodiversity hotspots. Consequently, the need of further herpetological investigations in this region of ecological importance is stressed.
... In ovoviviparous species, young develop lecithotrophically in eggs that hatch inside the female's reproductive tract, emerging as live young (Metallinou et al. 2016). Regular lecithotrophy is characteristic of the Striped Skink T. striata and Cape Skink T. capensis, while the Damara Variable Skink T. damarana and Western Threestriped Skink T. occidentalis are oviparous or viviparous (Vitt and Blackburn 1983;Branch 1998;Alexander and Marais 2007;Weinell and Bauer 2018). Weinell et al. (2019) provide insight into Trachylepis reproductive mode evolution based on a species-level phylogeny. ...
... Such large clutch/brood sizes have not been previously recorded (Visser 1975;Vitt and Blackburn 1983;Pianka 1986;Goldberg 2006 Branch (1998) only provided data for "southern populations", presumably referring to what are now T. striata and T. punctatissima. **There is uncertainty regarding the reproductive mode given that this taxon was recently realised to represent a species complex (Weinell & Bauer 2018). Table 2. Clutch/brood size in Trachylepis species recorded in various habitats and seasons in Namibia. ...
... Sequence of the mitochondrial (mtDNA) 16S ribosomal RNA gene from a tissue sample of the newly collected specimen were generated by Weinell & Bauer (2018) (GenBank accession number MG605669.1). This sequence was compared to the only other available T. megalura 16S sequence on GenBank (accession number KU236715.1), ...
... obs.). The 16S region of mtDNA has proved to be useful for identifying species-level divergences in the genus Trachylepis (Mausfeld et al. 2000;Ceríaco et al. 2016c;Allen et al. 2017;Weinell & Bauer 2018). ...
Angola and the Democratic Republic of the Congo are relatively unknown in terms of their herpetological diversity. Based on specimens collected in the Congolese region of the Katanga and the northeast of Angola during the first decades of the twentieth century, de Witte and Laurent independently suggested, based on morphological and coloration differences, that populations of T. megalura of these regions could belong a new "race". We compared specimens of T. megalura (including the type specimens of T. megalura and T. massaiana) with Angolan and Katangan museum specimens as well as newly collected specimens from Angola. Coloration pattern and morphological characters, in combination with substantial divergence in the 16S mitochondrial gene, confirm the distinctiveness of the west Central African form, and it is here described as a new species. Data regarding its natural history, ecology and global distribution are presented.
... Other novelties included the description of the lacertids Pedioplanis haackei and P. huntleyi (Conradie et al. 2012a and the cordylid Cordylus namakuiyus (Stanley et al. 2016). Some subspecies were validated as full species, including the geckos R. boultoni benguellensis and R. boultoni montanus (Ceríaco et al. 2016a) and the snake Psammophylax rhombeatus ocellatus (Branch et al. 2019), as well as the revival of the skink Trachylepis damarana from the synonymy of T. varia (Weinell and Bauer 2018). Some species, e.g. ...
... In addition, preliminary studies have revealed numerous problematic specimens and populations that demonstrate the existence of cryptic, previously synonymised species or unnamed taxa awaiting description in numerous genera. Geckos -Hemidactylus, Rhoptropus (Ceríaco et al. 2016a;Bauer and Kuhn 2017), Afroedura , and various Pachydactylus groups Ceríaco et al. 2016a;Heinz 2011); within the lacertids Nucras, Pedioplanis and Heliobolus (Branch and Tolley 2017); and a skink in the Trachylepis varia complex (Weinell and Bauer 2018). The descriptions of at least a dozen new species in these genera are in preparation. ...
This review summarises the current status of our knowledge of Angolan reptile diversity, and places it into a historical context of understanding and growth. It is compared and contrasted with known diversity in adjacent regions to allow insight into taxonomic status and biogeographic patterns. Over 67% of Angolan reptiles were described by the end of the nineteenth century. Studies stagnated during the twentieth century but have increased in the last decade. At least 278 reptiles are currently known, but numerous new discoveries have been made during recent surveys, and many novelties await description. Although lizard and snake diversity is currently almost equal, most new discoveries occur in lizards, particularly geckos and lacertids. Poorly known Angolan reptiles and others from adjacent regions that may occur in the country are highlighted. Most endemic Angolan reptiles are lizards and are associated with the escarpment and southwest arid region. Identification of reptile diversity hotspots are resolving but require targeted surveys for their delimitation and to enable protection. These include the Kaokoveld Centre of Endemism, Angolan Escarpment and the Congo forests of the north. The fauna of Angola remains poorly known and under-appreciated, but it is already evident that it forms an important centre of African reptile diversity and endemism.
... Variable skink (Fig. 3l Comments: Widespread in Africa and occurring in the eastern parts of South Africa (Beraduccii, Msuya, Howell & Ngalason, 2021a). A recent study has subdivided the T. varia complex into several distinct clades, but all material from southern and eastern South Africa is referred to the nominal form (Weinell & Bauer 2018). ...
Protected areas must be managed effectively if they are to contribute to reducing biodiversity loss, and one of the components of effective management is the development of biodiversity inventories. We conducted herpetofaunal surveys of the Mpofu-Fort Fordyce Nature Reserve complex in the Amathole District Municipality, Eastern Cape Province, South Africa. This study forms part of a series of rapid surveys to improve biodiversity inventory data of protected areas
within the province. Visual encounter survey methods and standard Y-shape trap arrays were used to conduct surveys in October–November 2014 and November 2016. A total of 35 species representing five Amphibia families (11 species), seven Sauria families (12 species), eightSerpentes families (11 species), and one Testudines family (one species) was recorded, amounting to 10 new reserve records and 18 new records at the Quarter Degree Square (QDS) scale. Although most of the species encountered are widespread and abundant, the considerable number of new QDS records confirm that our surveys have contributed to filling a data gap in this under-sampled area. The results of our surveys were consolidated with historic records and records from other recent surveys to produce an updated herpetofauna species list for the reserve complex. The consolidated list now documents 44 species for the reserve complex and 50 species for the two QDS.
... Climatic oscillations are thought to have driven cladogenesis and phylogeographic structuring in several southern African reptile taxa (Barlow et al., 2013;da Silva & Tolley, 2017;Diedericks & Daniels, 2013;Engelbrecht, vanNiekerk, Heideman, & Daniels, 2013;Stanley & Bates, 2014). In addition, divergence-time estimates have demonstrated that cladogenesis among southern African reptile taxa closely mirror periods characterized by climatic ameliorations throughout the Mio/Plio/Pleistocene (Kullenkampff, Van Zyl, Klaus, & Daniels, 2019;Medina et al., 2016;Tolley, Chase, & Forest, 2008;Weinell & Bauer, 2018). ...
We investigate the phylogeographic structure of a fossorial forest‐living snake species, the forest thread snake, Leptotyphlops sylvicolus Broadley & Wallach, 1997 by sampling specimens from the Eastern Cape and KwaZulu‐Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial sequence data (cyt b and ND4 ), along with population genetic analyses suggest the presence of phylogeographic breaks broadly congruent to those exhibited by other forest‐living taxa. Divergence‐time estimates indicate that cladogenesis within the study taxon occurred during the late Miocene climatic shifts, suggesting that cladogenesis was driven by habitat fragmentation. We further investigate the species‐level divergence within L . sylvicolus by including two partial nuclear loci (PRLR and RAG1 ). The three species delimitation methods (ABGD, bGMYC, and STACEY), retrieved 10–12 putative species nested within the L . sylvicolus species complex. These results were corroborated by iBPP implementing molecular and morphological data in an integrative Bayesian framework. The morphological analyses exhibit large overlap among putative species but indicate differences between grassland and forest species. Due to the narrow distributions of these putative species, the results of the present study have further implications for the conservation status of the L . sylvicolus species complex and suggest that forest and grassland habitats along the east coast of South Africa may harbor significantly higher levels of diversity than currently recognized.
... Divergence-time estimates indicate a late Miocene to early Pliocene cladogenesis within the A. pondolia species complex (Fig. 2.2). Cladogenesis during these periods corroborates the observations in several other lizard groups in southern Africa and along the Eastern Escarpment(Heinicke et al., 2017a;Medina et al., 2016;Stanley and Bates, 2014;Tolley et al., 2008;Weinell and Bauer, 2018). Within the Bradypodion chameleons, closed habitat species along the eastern escarpment and coastal region show comparatively similar timing of diversification where cladogenesis was initiated at the onset of the late Miocene through ...
This study investigates the phylogeographic structure of three co-distributed forest-living reptile species, the Pondo flat gecko (Afroedura pondolia), the forest thread snake (Leptotyphlops sylvicolus) and the Natal black snake (Macrelaps microlepidotus), by sampling specimens from the Eastern Cape and KwaZulu-Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial sequence data (ND4 and cyt b), along with population genetic analyses suggest the presence of broadly congruent biogeographic breaks among the study taxa. Sequence divergence values suggest that A. pondolia and L. sylvicolus represent species complexes comprising several cryptic species while M. microlepidotus exhibits population level differentiation. Divergence-time estimates indicate that cladogenesis within the study taxa occurred during the late Miocene to the Plio/Pleistocene climatic shifts, suggesting that cladogenesis was driven by climatic oscillations and suitable habitat fragmentation. We further investigate the species level divergence within A. pondolia and L. sylvicolus by including two partial nuclear loci (PRLR and RAG1) and employing several species delimitation methods (ABGD, bGMYC, PTP and STACEY). The species delimitation results were generally incongruent, estimating between two and 14 species nested within A. pondolia and between ten and 12 species nested within L. sylvicolus. In both taxa, the species hypotheses retrieved by STACEY based on the total-evidence data were preferred and used to define groups in the morphological analyses. In A. pondolia the multivariate morphological analyses indicate statistically significant differences among the four putative species, corroborating the presence of four species. In L. sylvicolus the morphological analyses exhibit large overlap among the ten putative species but indicate differences between grassland and forest species. The narrow distributions of the putative species identified in the present study have further implications for the conservation status of A. pondolia and L. sylvicolus and suggest that the fragmented forest habitat along the east coast of South Africa may harbor significantly higher levels of diversity than currently recognized.
... All values are statistically significant (p < 0.001). Escarpment (Heinicke et al., 2017a;Medina et al., 2016;Stanley and Bates, 2014;Tolley et al., 2008;Weinell and Bauer, 2018). Within the Bradypodion chameleons, closed habitat species along the eastern escarpment and coastal region show comparatively similar timing of diversification where cladogenesis was initiated at the onset of the late Miocene through the Pliocene and some recent cladogenesis in the Pleistocene (Tolley et al., 2008). ...
We assess the phylogeographic structure and test several species delimitation methods in the forest-living Pondo flat-gecko, Afroedura pondolia, by sampling specimens from across the entire distribution in the Eastern Cape and KwaZulu-Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial and nuclear DNA sequence data derived from four partial loci (ND4, cyt b, PRLR and RAG1), suggest the presence of four geographically discrete clades, which represent candidate species. We applied four species-delimitation methods (ABGD, bGMYC, PTP and STACEY), the results of which were largely incongruent in the number of putative species nested within A. pondolia. Multivariate morphological analyses indicate statistically significant differences among the four candidate species, corroborating the presence of four cryptic species within A. pondolia. Divergence-time estimates suggest that cladogenesis was driven by forest fragmentation from the late Miocene to the Plio/Pleistocene with the onset of more pronounced xeric climatic conditions causing forest fragmentation.
... specimens: BNP, main camp vicinity, -15.1271, 14.7715, 1246m, 26 July 2017BNP, main camp, -15.1016, 14.8399, 1224m, 27-28 July 2017BNP, main camp vicinity, -15.1028, 14.8477, 1241m, 28 July 2017BNP, on road to Nongalafa, -15.1274, 14.7714, 1225m, 30 July 2017Huíla Waterfall, -15.0549, 13.5349, 1658m, 5 August 2017Lubango, Cristo Rei, -14.9401, 13.5117, 2200m, 9 August 2017Lubango, -14.9434, 13.4644, 2012m, 10 August 2017 Comments.-The broadly distributed Trachylepis varia species complex was recently revised by Weinell and Bauer (2018), who suggested that specimens from central and northern Angola, Zambia, and southern Democratic Republic of the Congo likely correspond to Trachylepis albopunctata (Bocage, 1867). This clade was subsequently treated as T. cf. ...
... al., 2012; Karin et al., 2016; Metallinou et al., 2016;Weinell and Bauer, 2018). We used Muscle(Edgar, 2004) implemented in Geneious v6.1 to generate DNA sequence alignments. ...
... In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species (Barlow et al., 2013), and some putatively widely distributed species proved to be species complexes (Agama spp., Leaché, Wagner, et al., 2014; Hemidactylus fasciatus group, Leaché, Fujita, Minin, & Bouckaert, 2014;Wagner, Leaché, & Fujita, 2014;Naja melanoleuca complex, Wüster et al., 2018; Pelomedusa spp., Petzold et al., 2014;Vargas-Ramírez et al., 2010; Trachylepis varia complex, Weinell & Bauer, 2018), underlining the need of more research. Land tortoises (Testudinidae) are in this context of special interest because all species are considered to be imperilled. ...
In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species. With the present study, we contribute data for the leopard tortoise (Stigmochelys pardalis). It ranges from the Horn of Africa southward to South Africa and westwards to southern Angola. However, its natural occurrence is disputed for some southern regions. To clarify the situation, we used mtDNA sequences and 14 microsatellite loci from 204 individuals mainly from southern Africa. Our results retrieved five mitochondrial clades; one in the south and two in the north‐west and north‐east of southern Africa, respectively, plus two distributed further north. Using microsatellites, the southern clade matched with a well‐defined southern nuclear cluster, whilst the two northern clades from southern Africa corresponded to another nuclear cluster with three subclusters. One subcluster had a western and central distribution, another occurred mostly in the north‐east, and the third in a small eastern region (Maputaland), which forms part of a biodiversity hotspot. Genetic diversity was low in the south and high in the north of our study region, particularly in the north‐east. Our results refuted that translocations influenced the genetic structure of leopard tortoises substantially. We propose that Pleistocene climatic fluctuations caused leopard tortoises to retract to distinct refugia in southern and northern regions and ascribe the high genetic diversity in the north of southern Africa to genetic structuring caused by the survival in three refuges and subsequent admixture, whereas tortoises in the south seem to have survived in only one continuous coastal refuge.
... Comments.-There are several cryptic species within the taxon currently known as Trachylepis varia, and the Angolan material is not referable to true varia (Weinell and Bauer, 2018). The name albopunctata may represent the Angolan population, although confusion with other available names and limited data on the distribution of different lineages precludes definitive conclusions at this time (see Marques et al., in press). ...
... It is common throughout Zambia (Broadley 1971a). Recently split from the larger Trachylepis varia complex by Weinell and Bauer (2018). ...
The herpetofauna of Zambia has been relatively well-studied, although most surveys were conducted decades ago. In western Zambia in particular, surveys were largely restricted to a few centers, particularly those along the Zambezi River. We here report on the herpetofauna of the Ngonye Falls and surrounding regions in southwestern Zambia. We recorded 18 amphibian, one crocodile, two chelonian, 22 lizard, and 19 snake species, although a number of additional species are expected to occur in the region based on their known distribution and habitat preferences. We also provide three new reptile country records for Zambia (Long-tailed Worm Lizard, Dalophia longicauda, Anchieta's Worm Lizard, Monopeltis anchietae, and Zambezi Rough-scaled Lizard, Ichnotropis grandiceps), and report on the second specimen of Schmitz's Legless Skink, Acontias schmitzi, a species described in 2012 and until now known only from the holotype. This record also represents a 140 km southward range extension for the species.
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
This work is the second report of the results obtained from a series of rapid biodiversity surveys of the upper Cuito, Cubango, Cuando, Zambezi, and Kwanza River basins in Angola, which were conducted between 2015 and 2019 in conjunction with the National Geographic Okavango Wilderness Project. The herpetofauna of this region are poorly documented and the results of these surveys help to address the
knowledge gap regarding the conservation importance of this region. Here, an updated checklist is provided for the current and historical records of lizards, chelonians, and crocodiles from the southeastern region of Angola. A total of 369 new records were documented comprising 40 species, bringing the total number of
recognized lizard, chelonian, and crocodile species in this region to 58. These surveys documented four new country records (i.e., Lygodactylus chobiensis, Agama armata, Pachydactylus wahlbergii, and Ichnotropis cf. grandiceps) and increased the total number of reptile species known to occur in Angola (excluding snakes)
from approximately 157 to 161. Finally, updated distribution maps for the whole country are provided for all of the species encountered in this study.
Francisco Newton’s zoological expedition to Angola undertaken between 1903 and 1906 is one of the least studied of the naturalist’s life. Only three major papers regarding the herpetofauna collected in this expedition have been published, and a significant part of the specimens remains unstudied since the 1900’s. Here we review the extant herpetological specimens of this expedition, present an updated taxonomic revision, and provide new insights on their taxonomic status. The extant collection is constituted by 329 specimens (155 amphibians and 174 reptiles), corresponding to 73 species, 39 genera and 22 families, and it is presently housed in the Museu de História Natural e da Ciência da Universidade do Porto (MHNC-UP).
The first herpetological surveys of two mountains in northern Mozambique, Mount Lico and Mount Socone, are presented. A total of 19 species of amphibians (two orders, eight families, and 11 genera) and 21 species of reptiles (two orders, 11 families, and 17 genera) were recorded. Mount Lico is a unique site with representatives of both moist evergreen forest and miombo woodland herpetofaunal species. Noteworthy records for Mount Lico include an undescribed species of Arthroleptis, and a Lygodactylus that either represents a range extension of L. regulus or an undescribed species. Similarly, the Nothophryne found at the base of Mount Lico either represents a range extension of N. baylissi or an undescribed species. The finding of a Mertensophryne from the base of Mount Lico is reported and taxonomic confusion between M. anotis and M. loveridgei is highlighted. The findings presented here show that Mount Socone has a similar herpetofaunal composition to Mount Namuli, including the Pygmy Chameleon, Rhampholeon tilburyi, which was previously thought to be restricted to the latter mountain. A new species of Breviceps was found on Mount Socone, and the record of Arthroleptis aff. francei represents either a range extension for A. francei or an undescribed species. This survey provides a small but important contribution to the knowledge of Mozambican herpetofauna and biodiversity in general. Resumo.-Apresentamos os primeiros levantamentos herpetológicos de duas montanhas no norte de Moçambique, o Monte Lico e o Socone. Registamos um total de 19 espécies de anfíbios (duas ordens, oito famílias e 11 gêneros) e 21 espécies de répteis (duas ordens, 11 famílias e 17 gêneros). O Monte Lico é um local único, com representantes de herpetofauna de florestas húmidas e de miombo. Registos importantes para o Monte Lico incluem uma espécie não descrita de Arthroleptis, um Lygodactylus que representa uma extensão da distribuição de L. regulus ou uma espécie não descrita. Da mesma forma, o Nothophryne encontrado na base do Monte Lico representa uma extensão da distribuição de N. baylissi ou uma espécie não descrita. Nós relatamos a descoberta de um Mertensophryne da base do Monte Lico e destacamos a confusão taxonômica entre M. anotis e M. loveridgei. Nossas descobertas mostram que o Monte Socone tem uma composição de herpetofauna semelhante ao Monte Namuli, incluindo o camaleão-pigmeu Rhampholeon tilburyi, que antes se pensava estar restrito à última montanha. Uma nova espécie de Breviceps foi encontrada no Monte Socone, e o registo de Arthroleptis aff. francei representa uma extensão de distribuição para A. francei ou uma espécie não descrita. Esta é uma pequena mas importante contribuição para o conhecimento da herpetofauna moçambicana e da biodiversidade em geral.
O estado actual do conhecimento sobre a diversidade dos répteis
de Angola é aqui tratada no contexto da história da investigação herpetológica
no país. A diversidade de répteis é comparada com a diversidade
conhecida em regiões adjacentes de modo a permitir esclarecer questões
taxonómicas e padrões biogeográficos. No final do século xix, mais de
67% dos répteis angolanos encontravam‑se
descritos. Os estudos estagnaram
durante o século seguinte, mas aumentaram na última década.
Actualmente, são conhecidos pelo menos 278 répteis, mas foram feitas
numerosas novas descobertas durante levantamentos recentes e muitas
espécies novas aguardam descrição. Embora a diversidade dos lagartos e
das cobras seja praticamente idêntica, a maioria das novas descobertas
verifica‑se
nos lagartos, particularmente nas osgas e lacertídeos. Destacam‑se aqui os répteis angolanos mal conhecidos e outros de regiões adjacentes que possam ocorrer no país. A maioria dos répteis endémicos angolanos é constituída por lagartos e encontra‑se associada à escarpa e à região árida do Sudoeste. Está em curso a identificação de hotspots de diversidade de répteis, mas esta requer levantamentos direccionados para a sua delimitação e que garantam uma protecção concreta. Estes incluem o centro de endemismo do Kaokoveld, a escarpa de Angola e as florestas do Congo no Norte. A fauna angolana permanece pouco conhecida e subestimada, mas já é evidente que constitui um importante centro de diversidade e endemismo para os répteis africanos.
We here describe the first Neogene record of the squamate clade Mabuyidae. Although this clade has a cosmopolitan distribution today, no pre-Quaternary fossil record of these reptiles has so far been documented. The material comes from the locality Solnechnodolsk (Russia) and is dated to the late Miocene (MN 13). Although it comprises only jaw elements, it constitutes the first evidence of the occurrence of fossil skinks around the area of the Black Sea. The material is identical to Heremites vittatus, showing the existence of this lineage as early as the late Miocene. Thus, it may be used as a potential calibration point for further studies. The comparative anatomy of the structures of lower jaw in selected scinco-morph taxa with a special reference to Mabuya group is presented. The closure of the Meckelian canal is the condition at the basal node of the clade Sphenomorphidae + Eugongylidae + Egerniidae + Mabuyidea, whereas the closed canal in Acontias (Acontidae) evolved independently. However, Sphenomorphidae (Asymblepharus and Scin-cella) + Eugongylidae (Ablepharus) retain a large anterior opening of the Meckelian canal, whereas only a small opening characterizes the basal node of Egerniidae and Mabuyidae, except for H. vittatus and H. septemtaeniatus. The closure of the Meckelian canal in these two taxa is less well developed in comparison with other mabuyid skinks. Thus, a heterochronic pedomorphic process might have played a role in the evolution of these skinks. The Meckelian canal condition supports the monophyly of Heremites.
A list of 60 species of amphibians and reptiles found during a six-week survey in western Zambia is presented. Two species of amphibians are newly reported for Zambia: Amietia chapini and an undescribed species of Tomopterna, previously known to occur in the Democratic Republic of Congo and in Namibia, respectively. Some of the material collected could not be confidently identified to species level because of the taxonomic complexity and uncertainty of some groups (e.g., Phrynobatrachus, Ptychadena), even with the use of DNA barcoding. This list is a small contribution to the growing knowledge of Zambian and African herpetology.
Most mammals and approximately 20% of squamates (lizards and snakes) are viviparous, whereas all crocodilians, birds and turtles are oviparous. Viviparity evolved greater than 100 times in squamates, including multiple times in Mabuyinae (Reptilia: Scincidae), making this group ideal for studying the evolution of nutritional patterns associated with viviparity. Previous studies suggest that extreme matrotrophy, the support of virtually all of embryonic development by maternal nutrients, evolved as many as three times in Mabuyinae: in Neotropical Mabuyinae (63 species), Eumecia (2 species; Africa) and Trachylepis ivensii (Africa). However, no explicit phylogenetic hypotheses exist for understanding the evolution of extreme matrotrophy. Using multilocus DNA data, we inferred a species tree for Mabuyinae that implies that T. ivensii (here assigned to the resurrected genus Lubuya) is sister to Eumecia, suggesting that extreme matrotrophy evolved only once in African mabuyine skinks. © 2016 The Author(s) Published by the Royal Society. All rights reserved.
A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different
organisms is decribed. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat,
barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification.
The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even in low
technology laboratories. The amount of tissue required by this method is ∼50–100 mg. The quantity and the quality of the DNA
extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation
techniques such as restriction digestion, Southern blot and cloning.
The scincid genus Trachylepis is represented in the oceanic islands of the Gulf of Guinea by four species, Trachylepis maculilabris, T. affinis, T. adamastor and T. ozorii. Here we describe two new species, Trachylepis thomensis sp. nov., endemic to São Tomé Island and Rolas Islet, and Trachylepis principensis sp. nov., endemic to Príncipe Island. Phylogenetic analysis using the mitochondrial gene 16S shows that both new species are genetically divergent and reciprocally monophyletic, and confirms evidence for the uniqueness of these lineages presented in previous studies. Morphological data (scalation and morphometry) identify consistent phenotypic differences between these two island species. We were also able to confirm that the T. affinis population of Príncipe Island is conspecific with the African mainland population and most probably the result of recent introductions. These findings raise the number of known Trachylepis species in the Gulf of Guinea islands group to five, four of which are endemic, although the phylogenetic and phylogeographic relationships of T. adamastor and T. ozorii remain unknown and require further investigation.
The herpetofauna of Mozambique remains poorly documented despite recent surveys. We present here the first report on the herpetofauna occurring in Parque Nacional de Banhine in Gaza Province.Four chelonian, 13 snake, one amphisbaenid, 16 lizard and 15 frog species were recorded in the park, while an additional six snake, five lizard and two frog taxa have been recorded in close proximity and probably also occur in the park. Numerous range extensions are recorded, and these are discussed in the light of our present knowledge of the distribution of herpetofauna in Mozambique.
The Liolaemus alticolor group (Iguania: Tropiduridae) currently includes two or three species of morphologically similar, small-bodied lizards distributed from southern Peru and Bolivia to northern Argentina and Chile. Recently, a few populations of L. alticolor from northwestern Argentina were reported to be reproductively bimodal - having both oviparous and viviparous females at the same locality. We reexamined lizards from these putatively bimodal populations and found evidence that these populations include two sympatric yet distinct species - one oviparous, the other viviparous. These species can also be distinguished from L. alticolor sensu stricto from the type locality (Tiahuanaco, Bolivia). Here we describe the two new species, L. ramirezae and L. pagaburoi, from the province of Tucuman, Argentina. Liolaemus ramirezae differs from L. alticolor in having distinct neck folds, precloacal pores in females, and an oviparous reproductive mode, and in lacking both spots on the throat in males and a vertebral line. Liolaemus pagaburoi differs from L. alticolor in having distinct paravertebral markings, slender dorsal stripes, and more rugose head scales. Recognition of these new species as distinct resolves the paradox of reproductive bimodality in L. alticolor. Interestingly, both of the new species appear to be microhabitat specialists that associate with a single species of plant in their respective habitats. As predicted by the cold-climate hypothesis, the oviparous species is distributed in a warmer climate than is the viviparous species.
The herpetofauna of Mozambique remains poorly documented despite several recent surveys. This paper presents additional distribution records for a number of species from Mozambique, based on recent field excursions and older material at the Ditsong National Museum of Natural History. The new records suggest that a number of taxa are more widely distributed in southern Mozambique than is currently known while the additional material suggests that the taxonomy of some species requires further research.
In 1996, the U.S. Geological Survey (USGS) developed a global topographic elevation model designated as GTOPO30 at a horizontal resolution of 30 arc-seconds for the entire Earth. Because no single source of topographic information covered the entire land surface, GTOPO30 was derived from eight raster and vector sources that included a substantial amount of U.S. Defense Mapping Agency data. The quality of the elevation data in GTOPO30 varies widely; there are no spatially-referenced metadata, and the major topographic features such as ridgelines and valleys are not well represented. Despite its coarse resolution and limited attributes, GTOPO30 has been widely used for a variety of hydrological, climatological, and geomorphological applications as well as military applications, where a regional, continental, or global scale topographic model is required. These applications have ranged from delineating drainage networks and watersheds to using digital elevation data for the extraction of topographic structure and three-dimensional (3D) visualization exercises (Jenson and Domingue, 1988; Verdin and Greenlee, 1996; Lehner and others, 2008). Many of the fundamental geophysical processes active at the Earth's surface are controlled or strongly influenced by topography, thus the critical need for high-quality terrain data (Gesch, 1994). U.S. Department of Defense requirements for mission planning, geographic registration of remotely sensed imagery, terrain visualization, and map production are similarly dependent on global topographic data.
Since the time GTOPO30 was completed, the availability of higher-quality elevation data over large geographic areas has improved markedly. New data sources include global Digital Terrain Elevation Data (DTED®) from the Shuttle Radar Topography Mission (SRTM), Canadian elevation data, and data from the Ice, Cloud, and land Elevation Satellite (ICESat). Given the widespread use of GTOPO30 and the equivalent 30-arc-second DTED® level 0, the USGS and the National Geospatial-Intelligence Agency (NGA) have collaborated to produce an enhanced replacement for GTOPO30, the Global Land One-km Base Elevation (GLOBE) model and other comparable 30-arc-second-resolution global models, using the best available data. The new model is called the Global Multi-resolution Terrain Elevation Data 2010, or GMTED2010 for short. This suite of products at three different resolutions (approximately 1,000, 500, and 250 meters) is designed to support many applications directly by providing users with generic products (for example, maximum, minimum, and median elevations) that have been derived directly from the raw input data that would not be available to the general user or would be very costly and time-consuming to produce for individual applications. The source of all the elevation data is captured in metadata for reference purposes. It is also hoped that as better data become available in the future, the GMTED2010 model will be updated.
MAUSFELD-LAFDHIYA P., SCHMITZ A., INEICH I. & CHIRIO L., 2004 - Genetic variation in two African Euprepis species (Reptilia, Scincidae), based on maximum-likelihood and Bayesian analysis: taxonomic and biogeographic conclusions. Bonn. zool. Beitr, 52: 159-177.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
Many ecological and evolutionary studies seek to explain patterns of shape variation and its covariation with other variables. Geometric morphometrics is often used for this purpose, where a set of shape variables are obtained from landmark coordinates following a Procrustes superimposition.We introduce geomorph: a software package for performing geometric morphometric shape analysis in the r statistical computing environment.Geomorph provides routines for all stages of landmark-based geometric morphometric analyses in two and three-dimensions. It is an open source package to read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform statistical analyses of shape variation and covariation, and to provide graphical depictions of shapes and patterns of shape variation. An important contribution of geomorph is the ability to perform Procrustes superimposition on landmark points, as well as semilandmarks from curves and surfaces.A wide range of statistical methods germane to testing ecological and evolutionary hypotheses of shape variation are provided. These include standard multivariate methods such as principal components analysis, and approaches for multivariate regression and group comparison. Methods for more specialized analyses, such as for assessing shape allometry, comparing shape trajectories, examining morphological integration, and for assessing phylogenetic signal, are also included.Several functions are provided to graphically visualize results, including routines for examining variation in shape space, visualizing allometric trajectories, comparing specific shapes to one another and for plotting phylogenetic changes in morphospace.Finally, geomorph participates to make available advanced geometric morphometric analyses through the r statistical computing platform.
Supported by NASA's Earth Surface and Interior (ESI) Program, we are producing a global set of Ground Control Points (GCPs) derived from the Ice, Cloud and land Elevation Satellite (ICESat) altimetry data. From February of 2003, to October of 2009, ICESat obtained nearly global measurements of land topography (+/- 86° latitudes) with unprecedented accuracy, sampling the Earth's surface at discrete ~50 m diameter laser footprints spaced 170 m along the altimetry profiles. We apply stringent editing to select the highest quality elevations, and use these GCPs to characterize and quantify spatially varying elevation biases in Digital Elevation Models (DEMs). In this paper, we present an evaluation of the soon to be released Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010). Elevation biases and error statistics have been analyzed as a function of land cover and relief. The GMTED2010 products are a large improvement over previous sources of elevation data at comparable resolutions. RMSEs for all products and terrain conditions are below 7 m and typically are about 4 m. The GMTED2010 products are biased upward with respect to the ICESat GCPs on average by approximately 3 m.
We provide descriptions for two new cryptic species belonging to the Liolaemus alticolor group from northern Argentina and northeastern Chile. The new species were previously considered conspecific with either Liolaemus walkeri in northeastern Chile or L. alticolor in northwestern Argentina and adjacent Chile. However, the new species differ from these taxa, and all other members of the alticolor group, in a number of characteristics. Liolaemus chaltin n. sp. differs from L. alticolor from the type locality (Tiahuanaco, Bolivia) in the following ways: this new species has a larger body size; a fragmented vertebral stripe; and a pigmented subocular (white in L. alticolor), and is one of just three members of the alticolor group that is oviparous. Liolaemus puna n. sp. differs from all other members of the alticolor group in that male L. puna lack paravertebral markings and dorsolateral and vertebral stripes. Females, however, are similar to other members of the alticolor group but can be distinguished from them by several meristic characters. Liolaemus puna is widely distributed throughout the high-elevation (3680–4400 m) Puna regions (a flat or gently sloping steppe dominated by perennial bunch grasses and small shrubs) in northwestern Argentina and northeastern Chile. Liolaemus chaltin is known only from the Puna of central Jujuy Province, Argentina (3400–3750 m). Based on examina-tions of the type series of L. alticolor and L. walkeri, we determined that virtually all northern Chilean populations of Liolaemus previously considered to belong to either of these two species should be assigned to L. puna. Thus, the range of L. alticolor is restricted to Bolivia and southern Perú , and the range of L. walkeri is restricted to central and southern Andean Perú. Liolaemus chaltin is oviparous, and L. puna is viviparous, and because both are morphologically similar to L. alticolor, some inves-tigators have suggested that some populations of L. alticolor may be reproductive bimodal. Our studies, however, indicate that these populations represent sympatric populations of the cryptic species described herein. A diagnostic key is provided for the currently recognized members of the alticolor group. En este trabajo presentamos la descripció n de dos nuevas especies pertenecientes al grupo Liolaemus alticolor del norte de Argentina y nordeste de Chile. Las nuevas especies fueron consideradas previamente como conespecíficas con Liolaemus wal-keri en el noreste de Chile, o L. alticolor en el noroeste de Argentina y areas limi-tantes de Chile. En efecto, las nuevas especies difieren de estos taxa y de todos los otros miembros del grupo alticolor en varios caracteres morfoló gicos y bioló gicos. Liolaemus chaltin n. sp. difiere de L. alticolor de la localidad tipo (Tiahuanaco, Bo-livia) de la siguiente forma: es de mayor tamaño, la línea vertebral fragmentada, la subocular pigmentada, y es uno de los tres miembros del grupo que es ovíparo. Liolaemus puna n. sp. difiere de todos los otros miembros del grupo alticolor en que los machos de esta especie carecen de bandas dorsolaterales, manchas paraverte-brales, y de linea vertebral. Las hembras son similares a las de las restantes especies del grupo aunque pueden diferenciarse mediante diferentes caracteres meristicos. Liolaemus puna está ampliamente distribuido en las regiones de considerable ele-vació n (3680–4400) de la Puna (una estepa carente de arboles y caracterizada por la presencia de pastizales perennes y pequeños arbustos) en el norte de Argentina y noreste de Chile. Liolaemus chaltin es conocido solamente en la Puna de la región central y norte de la provincia de Jujuy, Argentina (3400–3750 m). Basados en el estudio de las series tipo de L. alticolor y L. walkeri, hemos determinado que casi todas las poblaciones del norte de Chile de Liolaemus previamente consideradas como una u otra de esas dos especies deberían ser asignadas a L. puna. De este modo el rango de L. alticolor se limita a Bolivia y sur del Perú, y el rango de L. walkeri esta limitado a los Andes del sur y centro de Perú. Liolaemus chaltin es
The evolution and subsequent ecological expansion of grasses (Poaceae) since the Late Cretaceous have resulted in the establishment of one of Earth's dominant biomes, the temperate and tropical grasslands, at the expense of forests. In the past decades, several new approaches have been applied to the fossil record of grasses to elucidate the patterns and processes of this ecosystem transformation. The data indicate that the development of grassland ecosystems on most continents was a multistage process involving the Paleogene appearance of (C3 and C4) open-habitat grasses, the mid-late Cenozoic spread of C3 grass-dominated habitats, and, finally, the Late Neogene expansion of C4 grasses at tropical-subtropical latitudes. The evolution of herbivores adapted to grasslands did not necessarily coincide with the spread of open-habitat grasses. In addition, the timing of these evolutionary and ecological events varied between regions. Consequently, region-by-region investigations using both direct (plant fossil...
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Significant contributions to the poorly known reptile fauna of northern Mozambique were made during a biodiversity survey of the Niassa Game Reserve (NGR), situated in northern Mozambique, bordering Tanzania. Of approximately 100 reptile species currently known from northern Mozambique, 57 species were recorded from the NGR. Important discoveries included: a new species of girdled lizard (Cordylus sp.) in rock cracks on the summit outcrops of Serra Mecula; the first national records of Melanoseps sp. and Lygodactylus angularis (both isolated populations are atypical and further studies are required to assess their taxonomic status); the first records for northern Mozambique for Chirindia swynnertoni, Lygodactylus chobiensis, Pachydactylus punctatus, Elasmodactylus tetensis, and Latastia johnstoni; the most northerly records of Pachydactylus punctatus, Agama kirkii, and Gerrhosaurus vallidus; an unusual population of Bitis arietans whose taxonomic status require further analysis; and a population of Cycloderma frenatum in the Lugenda River that fills a large gap in the species' known distribution.
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum, and maximum temperature. Input data were gathered from a variety of sources and, where possible, were restricted to records from the 1950-2000 period. We used the thin-plate smoothing spline algorithm implemented in the ANUSPLIN package for interpolation, using latitude, longitude, and elevation as independent variables. We quantified uncertainty arising from the input data and the interpolation by mapping weather station density, elevation bias in the weather stations, and elevation variation within grid cells and through data partitioning and cross validation. Elevation bias tended to be negative (stations lower than expected) at high latitudes but positive in the tropics. Uncertainty is highest in mountainous and in poorly sampled areas. Data partitioning showed high uncertainty of the surfaces on isolated islands, e.g. in the Pacific. Aggregating the elevation and climate data to 10 arc min resolution showed an enormous variation within grid cells, illustrating the value of high-resolution surfaces. A comparison with an existing data set at 10 arc min resolution showed overall agreement, but with significant variation in some regions. A comparison with two high-resolution data sets for the United States also identified areas with large local differences, particularly in mountainous areas. Compared to previous global climatologies, ours has the following advantages: the data are at a higher spatial resolution (400 times greater or more); more weather station records were used; improved elevation data were used; and more information about spatial patterns of uncertainty in the data is available. Owing to the overall low density of available climate stations, our surfaces do not capture of all variation that may occur at a resolution of 1 km, particularly of precipitation in mountainous areas. In future work, such variation might be captured through knowledge-based methods and inclusion of additional co-variates, particularly layers obtained through remote sensing.
As the fields of molecular systematics and phylogeography are advancing, it is necessary to incorporate multiple loci in both population and species-level inference. Here, we present primer sets for 104 intronless orthologus exons designed for amplification in all squamates. When comparing the Anolis genome to the Gallus genome, all the markers have less than 67.2% DNA sequence identity, the percent identity of the first third of the commonly used nuclear marker RAG-1. The rate of evolution in these markers is therefore greater than nuclear markers commonly used, and we demonstrate their usefulness for both phylogeographic and phylogenetic studies.
Improvements in technology have reduced the cost of DNA sequencing to the point that the limiting factor for many experiments is the time and reagent cost of sample preparation. We present an approach in which 192 sequencing libraries can be produced in a single day of technician time at a cost of about $15 per sample. These libraries are effective not only for low-pass whole-genome sequencing, but also for simultaneously enriching them in pools of approximately 100 individually barcoded samples for a subset of the genome without substantial loss in efficiency of target capture. We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study.
Phylogeographic patterns in wide-ranging species in southern Africa remain largely unexplored, especially in areas north of South Africa. Here, we investigate population structuring, demographic history, and the colonization pattern of the western rock skink (Trachylepis sulcata), a rock-dwelling species with a range extending from southwestern South Africa into Angola. Using 1056 bp from the mitochondrial marker ND2 and > 2.5 kb from three nuclear genes (EXPH5, KIF24, RAG-1), we constructed allele networks, generated extended Bayesian skyline plots and performed population clustering analyses. Analyses of historical demographic patterns show an overall southward range expansion from Northern Namibia into Southern Namibia and South Africa, although we find contrasting genetic breaks across these geographic regions using nuclear and mitochondrial data. We suggest that mtDNA has introgressed across a nuclear break corresponding to the Knersvlakte region of South Africa, a previously proposed biogeographic barrier for rupicolous species. This pattern of mitochondrial variation contrasts sharply to that of other South African taxa previously investigated, which all show significant mtDNA differentiation across the Knersvlakte region. Additionally, while other taxa show divergences dating to the Pliocene, T. sulcata appears to be a recent arrival in southern Africa, having crossed this barrier and colonized South Africa in the mid-Pleistocene. The complex phylogeographic history of T. sulcata corroborates the intricate patterns of genetic variation found in South African taxa and provides novel insight into historical processes affecting species distributed across Namibia.
The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface.
The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA–RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA
tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de.
Contact zones between two evolutionary lineages are often useful for understanding the process of speciation
because the observed genetic pattern reflects the history of differentiation. The Eurasian lacertid lizard Zootoca
vivipara is a potentially interesting model for studying the role of reproductive mode in the speciation of squamate
reptiles because it has both oviparous (Zootoca vivipara carniolica) and viviparous (Zootoca vivipara vivipara)
populations that have recently been shown to be genetically distinct. We studied a newly-discovered syntopic area
of these two Zootoca subspecies in the central Italian Alps using genetic markers to investigate the level of
introgression between them. Patterns of genetic differentiation in a fragment of the mitochondrial DNA cytb gene
and a set of nuclear microsatellites show that the speciation process is complete in this area, with no evidence of
recent introgression. Phylogenetic and genotypic divergence suggests that the two subspecies have experienced
long independent evolutionary histories, during which genetic and phenotypic differences evolved. The possible
roles of biogeography, reproductive mode, and cytogenetic differentiation in this speciation process are discussed.
A wide range of modelling algorithms is used by ecologists, conservation practitioners, and others to predict species ranges from point locality data. Unfortunately, the amount of data available is limited for many taxa and regions, making it essential to quantify the sensitivity of these algorithms to sample size. This is the first study to address this need by rigorously evaluating a broad suite of algorithms with independent presence-absence data from multiple species and regions. We evaluated predictions from 12 algorithms for 46 species (from six different regions of the world) at three sample sizes (100, 30, and 10 records). We used data from natural history collections to run the models, and evaluated the quality of model predictions with area under the receiver operating characteristic curve (AUC). With decreasing sample size, model accuracy decreased and variability increased across species and between models. Novel modelling methods that incorporate both interactions between predictor variables and complex response shapes (i.e. GBM, MARS-INT, BRUTO) performed better than most methods at large sample sizes but not at the smallest sample sizes. Other algorithms were much less sensitive to sample size, including an algorithm based on maximum entropy (MAXENT) that had among the best predictive power across all sample sizes. Relative to other algorithms, a distance metric algorithm (DOMAIN) and a genetic algorithm (OM-GARP) had intermediate performance at the largest sample size and among the best performance at the lowest sample size. No algorithm predicted consistently well with small sample size (n < 30) and this should encourage highly conservative use of predictions based on small sample size and restrict their use to exploratory modelling.
This edition supplements the 397 South African reptiles originally represented in this field guide by 64 new species. Some of these are new discoveries in the region, others are reclassifications. Author Bill Branch has also adapted the original text, modifying distributions and biology to reflect the most up-to-date research on the subject. The book covers 133 species of snake, as well as many and varied lizard and gecko species, tortoises, turtles, terrapins and the crocodile. New species entries introduce 13 gecko species, eight skinks and three snakes, amongst others. Each species entry includes size range, a physical description of the creature and a discussion on biology and breeding, habitat and range. Where subspecies occur, these are described. Each account is accompanied by a distribution map, which has been updated where necessary. Explanatory notes and a comprehensive glossary make the subject accessible to even the beginner herpretologist.
Data from spaceborne light detection and ranging (lidar) opens the
possibility to map forest vertical structure globally. We present a
wall-to-wall, global map of canopy height at 1-km spatial resolution,
using 2005 data from the Geoscience Laser Altimeter System (GLAS) aboard
ICESat (Ice, Cloud, and land Elevation Satellite). A challenge in the
use of GLAS data for global vegetation studies is the sparse coverage of
lidar shots (mean = 121 data points/degree2 for the L3C
campaign). However, GLAS-derived canopy height (RH100) values were
highly correlated with other, more spatially dense, ancillary variables
available globally, which allowed us to model global RH100 from forest
type, tree cover, elevation, and climatology maps. The difference
between the model predicted RH100 and footprint level lidar-derived
RH100 values showed that error increased in closed broadleaved forests
such as the Amazon, underscoring the challenges in mapping tall (>40
m) canopies. The resulting map was validated with field measurements
from 66 FLUXNET sites. The modeled RH100 versus in situ canopy height
error (RMSE = 6.1 m, R2 = 0.5; or, RMSE = 4.4 m,
R2 = 0.7 without 7 outliers) is conservative as it also
includes measurement uncertainty and sub pixel variability within the
1-km pixels. Our results were compared against a recently published
canopy height map. We found our values to be in general taller and more
strongly correlated with FLUXNET data. Our map reveals a global
latitudinal gradient in canopy height, increasing towards the equator,
as well as coarse forest disturbance patterns.
The taxonomy of twenty‐one evolutionary species of Mabuya from southeastern Africa is reviewed, using the general lineage concept and several diagnostic characters not previously used for this genus. This has resulted in two insular populations, M. casuarinae Broadley and M. albotaeniata Boettger (Pemba Island), being recognised as full species rather than subspecies of M. maculilabris (Gray). In addition, M. punctulata Bocage is given specific status, and in the M. striata complex the “subspecies” punctatissima (A. Smith), wahlbergii (Peters) and sparsa Mertens are recognised as distinct species and M. mlanjensis Loveridge is revived from synonymy.
POYNTON, J.C. 1997. On Bufo nyikae Loveridge and the B. lonnbergi complex of East African highlands (Anura: Bufonidac). Afr. J. Herpetol. 46(2): 98–102.Grandison (1972) and Tandy (1972) treated the Malawian Bufo taitanus nyikae Loveridge and the Kenyan B. lonnbergi nairobiensis Loveridge and B. mocquardi Angel as synonyms of B. lonnbergi Andersson. New material of the Nyikan Toad leads to a reassessment of the characters that suggested the synonymy; this in turn leads to a reconsideration of other material relegated to the synonymy of lonnbergi. It is concluded that nyikac is sufficiently distinct from all Kenyan material to merit specific status; separability of nairobiensis from mocquardi remains in doubt, but all this material is separable from lonnbergi. A single specimen of an apparently undescribed species from south-western Tanzania indicates the presence of this complex in Tanzanian highlands. Granting specific status to nyikae requires corrections to the zoogeographical treatment of the Zambesiaca region (poynton & Broadley 1991). B. nyikae is now regarded as a northern Malawi palaeoendemic.
Relationships of Mabuya lizards from the islands of the Gulf of Guinea where estimated using partial 12S rRNA, 16S rRNA and cytochrome b mitochondrial gene sequences. Mabuya maculilabris from São Tomé and Principe are discreet monophyletic units, highly divergent from each other and from mainland populations, indicating M. maculilabris may be a species complex. Mabuya affinis from Principe is similarly distinct from mainland populations of this species. The relationships of Mabuya ozorii from Annobon are unclear, but the three species in the Gulf of Guinea islands are not closely related, indicating multiple independent colonization events. The recent proposal to partition Mabuya into four genera is premature, since at least five distinct genetic lineages can be identified.
Saiphos equalis, a semi-fossorial scincid lizard from south-eastern Australia, is one of only three reptile species world-wide that are known to display geographic variation in reproductive mode. Uniquely, Saiphos equalis includes populations with three reproductive modes: oviparous with long (15-day) incubation periods; oviparous with short (5-day) incubation periods; and viviparous (0-day incubation periods). No Saiphos populations show 'normal' scincid oviparity (>30-day incubation period). We used mitochondrial nucleotide sequences (ND2 and cytochrome b) to reconstruct relationships among populations from throughout the species' distribution in New South Wales, Australia. Under the phylogenetic species concept, phylogenetic analyses are consistent with the oviparous and viviparous populations of S. equalis being conspecific. Phylogenetic analyses suggest that the long incubation period oviparous lineage is the sister group to all other populations; and that the viviparous populations belong to a cluster of weakly supported clades basal to the short-incubation-period oviparous clade. These clades correspond to variation in reproductive mode and geographic location.
The present aridity of Africa contrasts with the lush environments that existed over most of the continent in the early Cenozoic. The extinction of large terrestrial herbivores at the end of the Mesozoic, and relatively warm global climatic conditions in the early Cenozoic contributed to the spread of forests and woodlands in regions today occupied by grasslands and deserts. The increase in aridity after the Eocene climate optimum has been complex, characterized by multiple reversals and modulated by rifting in eastern Africa. The paleobotanical evidence indicates that ecological differentiation within the continent existed early in the Cenozoic, with some areas dominated by moist forests and others by drier Acacia woodlands. C4 grasslands began to spread during the Late Miocene, and became more prominent during the Pleistocene. In parallel to the spread of grassland mosaics during the Cenozoic there was an increase in the diversity of large herbivorous mammals (with body mass >350 kg). This diversity in megafauna peaked in the Pliocene. One of the key ecological roles of the megafauna was to create and maintain complex mosaics that included open habitats. Faunal evidence of paleoenvironments in the Turkana Basin of Kenya corroborates conclusions derived from other lines of evidence, but raises new questions. Hypsodont and cursorial bovids increased in abundance in the Late Miocene about 6 Ma, in the Pliocene after 3 Ma, and again in the Plio-Pleistocene after 2 Ma. But this faunal evidence also demonstrates that not all parts of the Turkana Basin responded in the same way to climatic changes. The lower Omo valley of Ethiopia, a northern extension of the Turkana Basin, remained significantly more forested than the areas near the western margins of the basin. Major river valleys like the Omo served as refuges and centers of endemism during intervals of significant climatic fluctuations. A similar role was played by the coastal and montane forests of eastern Africa, which were separated from the Central African forests by an arid corridor that stretched from northeast Africa to Namibia, and probably originated in the Miocene. The complex mosaic of environments in eastern Africa today continues to support an immensely diverse range of plants and animals, many of them found nowhere else on earth.
Sindaco, R., Metallinou, M., Pupin, F., Fasola, M. & Carranza, S. (2012). Forgotten in the ocean: systematics, biogeography and evolution of the Trachylepis skinks of the Socotra Archipelago. —Zoologica Scripta, 41, 346–362.
The Socotra Archipelago, in the north-west Indian Ocean, is considered to be one of the most remote and most biodiversity rich and distinct islands in the world. Often referred to as the ‘Galapagos of the Indian Ocean’, it was designated a UNESCO World Heritage Natural site in 2008. Despite having a very rich and bizarre fauna and flora with a high level of endemicity at both species and generic levels, the taxonomy of most of the groups is still not clear, and their origin and evolution remain unknown. Reptiles constitute the most relevant vertebrate fauna of the Socotra Archipelago, with 90% of the 30 species and 45% of the 12 genera being found nowhere else in the world. The skinks of the endemic species Trachylepis socotrana are the only reptile species in the Archipelago distributed across all four islands (Socotra, Darsa, Samha and Abd Al Kuri). Although the species is very well known from Socotra Island, it was not discovered on Samha until 1999 and on Darsa until 2000, whereas only a few citations and one single Museum specimen exist for the population from Abd Al Kuri. To clarify the systematics, biogeography and evolution of Trachylepis socotrana, we assembled a dataset for Mabuya sensu lato including 904 base pairs (bp) of sequence (392 bp from the 12S and 512 from the 16S rRNA mitochondrial genes) for 115 individuals, including specimens of T. socotrana from all four island populations, numerous representatives of the genus Trachylepis from the Middle East, Africa and Madagascar, plus some individuals from each of the other three genera of Mabuya sensu lato (Chioninia, Eutropis and Mabuya). The results of the phylogenetic analyses indicate that, contrary to what was previously thought, members of the genus Trachylepis have colonized the Socotra Archipelago in two independent events, with the first giving rise to the populations from Socotra, Samha and Darsa and the second to the Trachylepis from Abd Al Kuri Island. According to the calibrations, both colonization events occurred within the last fourteen million years, when the Socotra Archipelago had already drifted away from Arabia, thus ruling out vicariance. Both morphological and genetic data show that the Trachylepis from Abd Al Kuri is a distinct taxon, which is herein described as a new species belonging to the T. brevicollis species complex. On the basis of this evidence, the terrestrial herpetofauna from Abd Al Kuri is composed exclusively of endemic species (one of which, the gecko Pristurus abdelkuri, was introduced into some parts of Socotra).
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.
Viviparity has evolved from oviparity in many vertebrate lineages, and species that contain both oviparous and viviparous populations offer the best opportunity for a detailed examination of the processes involved in this major life-history transition. However, although several such species have been reported, none have been the subject of detailed phylogenetic analyses. We examine such a case within the Australian scincid lizard bougainvillii. Data were obtained by sequencing a 314-bp segment of mitochondrial cytochrome b from 32 individuals from 17 populations of L. bougainvillii and two morphologically similar congeneric species (L. dorsalis L. microtus). Sequences were aligned and analyzed using parsimony and distance methods. The resultant matriarchal phylogeny resolved the populations of L. bougainvillii into three major groups: a population from NSW; a group predominantly from Eyre Peninsula; and a less well-defined group from the central part of the species range. The NSW and Eyre Peninsula groups are oviparous and are quite divergent from other L. bougainvillii populations and from each other. The central group contains both viviparous and oviparous populations, and seem to represent a more recent radiation within the species. Our results indicate that viviparity has evolved at least twice within the genus Lerista, because the viviparous L. microtus is not closely related to viviparous populations of L. bougainvillii. The lack of phylogenetic separation of mtDNAs from viviparous and oviparous populations within L. bougainvillii relative to strong geographic structure within the latter indicates that populations with different reproductive modes are indeed conspecific. Lerista bougainvillii is thus the first vertebrate species for which intraspecific bimodality in reproductive mode can be claimed with any certainty.
A 487-bp fragment of the mitochondrial 16S rRNA gene was sequenced in 26 species of the circumtropical lizard genus Mabuya and used to analyze phylogenetic relationships within the genus. The species from Africa and Madagascar formed a monophyletic group relative to the included Asian and South American taxa. The Malagasy species included (M. elegans, M. cf. dumasi, and M. comorensis) did not appear as a monophylum. Combined and separate analysis of the 16S data and additional sequences of the mitochondrial 12S rRNA, ND4, and cytochrome b genes (a total of 2255 bp) in one Asian, two Malagasy, and two African species also did not result consistently in a monophyletic grouping of the Malagasy taxa. However, a monophylum containing African and Malagasy taxa was strongly supported by the combined analysis. These preliminary results indicate that Mabuya probably colonized Madagascar from Africa through the Mozambique Channel.