Achille P. Raselimanana

Phylogeny and evolution of Malagasy plated lizards

The endemic plated lizards (Gerrhosauridae) of Madagascar are one of the most diverse groups of lizards on the island (19 species) and are found in all ecoregions. On an island that presents so many interesting biological questions, plated lizards are an ideal group for examining patterns of diversification due to their high (but tractable) diversity and wide distribution. To resolve the taxonomy and evolutionary relationships of Malagasy plated lizards, and to explore their biogeographic history, we have generated a molecular phylogeny based on >2kb of both mitochondrial (cob, 1142 bp) and nuclear (NT-3, 419 bp; c-mos, 542 bp) DNA sequences. Phylogenetic relationships and divergence-time estimates indicate Zonosaurinae are monophyletic, arising from a single colonization event, likely from Africa to Madagascar in the Paleogene (Paleocene/early Eocene), with subsequent radiation. Furthermore, our results reveal widespread mischaracterization of species delimitation and assignment based on phenotypic characteristics. Paraphyly of a number of zonosaurine species was strongly supported by our dataset, revealing not only instances of likely cryptic species (phenotypic conservatism) but also phenotypic/genotypic discordance in the delimitation of species (phenotypic variability). These results clearly demonstrate the complex history of biotic diversification on Madagascar and provide novel insight into biogeographic patterns on the island.

Extinction Risks and the Conservation of Madagascar's Reptiles

Background An understanding of the conservation status of Madagascars endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the islands mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. Methodology/Principal Findings Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. Conclusions/Significance With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and western regions of Madagascar and this study highlights the importance of these arid regions to conserving the islands biodiversity.

Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (genus Oplurus)

Understanding the remarkably high species diversity and levels of endemism found among Madagascar’s flora and fauna has been the focus of many studies. One hypothesis that has received much attention proposes that Quaternary climate fluctuations spurred diversification. While spatial patterns of distribution and phylogenetic relationships can provide support for biogeographic predictions, temporal estimates of divergence are required to determine the fit of these geospatial patterns to climatic or biogeographic mechanisms. We use multilocus DNA sequence data to test whether divergence times among Malagasy iguanid lizards of the subfamily Oplurinae are compatible with a hypotheses of Pliocene–Pleistocene diversification. We estimate the oplurine species tree and associated divergence times under a relaxed‐clock model. In addition, we examine the phylogeographic structure and population divergence times within two sister species of Oplurus primarily distributed in the north‐west and south‐west of Madagascar (Oplurus cuvieri and Oplurus cyclurus, respectively). We find that divergence events among oplurine lineages occurred in the Oligocene and Miocene and are thus far older and incompatible with the hypothesis that recent climate fluctuations are related to current species diversity. However, the timing of intraspecific divergences and spatial patterns of population genetic structure within O. cuvieri and O. cyclurus suggest a role for both intrinsic barriers and recent climate fluctuations at population‐level divergences. Integrating information across spatial and temporal scales allows us to identify and better understand the mechanisms generating patterns diversity.

Protected area surface extension in Madagascar: Do endemism and threatened species remain useful criteria for site selection?

The ‘hotspot approach’ considers that endemism and threatened species are key factors in protected area designation. Three wetland and forest sites have been proposed to be included into Madagascar’s system of protected areas (SAPM – Systeme des Aires Protegees de Madagascar). These sites are Manambolomaty (14,701 ha) and Mandrozo (15,145 ha) in the west and Bemanevika (37,041 ha) in the north. Biodiversity inventories of these three sites recorded 243 endemic species comprised of 44 reptiles, 54 amphibians, 104 birds, 23 small mammals, 17 lemurs and one fish. Of these 243 species, 30 are threatened taxa comprising two Critically Endangered (CR), 11 Endangered (EN) and 17 Vulnerable (VU) species. The long term ecological viability of these sites has been shown by population stability of the two Critically Endangered flagship species, the Madagascar fish eagle (Haliaeetus vociferoides) in Manambolomaty and Mandrozo and the recently rediscovered Madagascar pochard (Aythya innotata) in Bemanevika. Other threatened species and high biological diversity also justifies their inclusion into Madagascar’s SAPM.

New Species of Day Gecko, Phelsuma Gray (Reptilia: Squamata: Gekkonidae), from the Réserve Naturelle Intégrale d'Andohahela, Southern Madagascar

Abstract Andohahela Réserve Naturelle Intégrale is located in southeastern Madagascar. It consists of three parcels, the largest of which (Parcel 1, 63,100 ha), lying on the eastern flank of the Anosyenne Mountains between 90 and 1972 m elevation, is dominated by rain forest. We surveyed the herpetofauna of Parcel 1 at the beginning of the warm, rainy season between 20 October and 5 December 1995. We recorded 45 amphibian and 32 reptile species in Parcel 1, including a new species of Phelsuma, which we describe in this paper. This new species, Phelsuma malamakibo, is a medium-sized, rock-dwelling species which occurs in primary rain forest at elevations between 810 m and 1940 m. It is identified by the presence of a distinct dark lateral stripe on the neck and body with a white lateral stripe beneath it and a second, thin dark lateral stripe below the white stripe; greenish dorsal ground color with reddish brown spots arranged into three longitudinal rows or lines on the neck and back; no sexual dichromatism; a median cleft dorsally on the rostral scale; nostrils centered above the first supralabial scale; subequal subcaudal scales; keeled gular and anterior chest scales; and smooth (unkeeled) scales on the ventral surfaces of the body and tail. In most respects, this new species is similar to Phelsuma lineata, P. pusilla, and P. quadriocellata; however, these species have keeled ventral scales. Phelsuma malamakibo is similar to P. modesta in having smooth ventral scales, but the latter species is sexually dichromatic and differs from P. malamakibo in details of coloration and nostril position, as well as habitat. Phelsuma modesta is largely arboricolous in variable, usually drier habitats, whereas P. malamakibo is saxicolous in rain forest.

A new black-bellied snake (Pseudoxyrhophiinae: Liophidium) from western Madagascar, with notes on the genus Pararhadinaea

We describe Liophidium maintikibo, a new species of pseudoxyrhophiine snake from the dry deciduous forest of Kirindy, western Madagascar. The new species is related to Liophidium therezieni but differs by a lower number of ventral scales and several details of colouration. Its ventral scales have a large central black patch which is missing from the subcaudals. This predominantly black ventral side is similar to that of another enigmatic Malagasy snake, Pararhadinaea melanogaster, for which we here present evidence for two new locality records, Ankarana and Daraina in northern Madagascar. The phylogenetic relationships of P. melanogaster (the sole representative of a monotypic genus) have so far not been clarified. Similarities to Liophidium maintikibo may indicate affinities to Liophidium ,b utP. melanogaster differs from this new species by a lower number of ventrals, subcaudals, number of maxillary teeth and by a different dorsal colouration.

Phylogeography and support vector machine classification of colour variation in panther chameleons

Lizards and snakes exhibit colour variation of adaptive value for thermoregulation, camouflage, predator avoidance, sexual selection and speciation. Furcifer pardalis, the panther chameleon, is one of the most spectacular reptilian endemic species in Madagascar, with pronounced sexual dimorphism and exceptionally large intraspecific variation in male coloration. We perform here an integrative analysis of molecular phylogeography and colour variation after collecting high‐resolution colour photographs and blood samples from 324 F. pardalis individuals in locations spanning the whole species distribution. First, mitochondrial and nuclear DNA sequence analyses uncover strong genetic structure among geographically restricted haplogroups, revealing limited gene flow among populations. Bayesian coalescent modelling suggests that most of the mitochondrial haplogroups could be considered as separate species. Second, using a supervised multiclass support vector machine approach on five anatomical components, we identify patterns in 3D colour space that efficiently predict assignment of male individuals to mitochondrial haplogroups. We converted the results of this analysis into a simple visual classification key that can assist trade managers to avoid local population overharvesting.

Multilocus phylogenetic and geospatial analyses illuminate diversification patterns and the biogeographic history of Malagasy endemic plated lizards (Gerrhosauridae: Zonosaurinae)

Although numerous studies have attempted to find single unifying mechanisms for generating Madagascars unique flora and fauna, little consensus has been reached regarding the relative importance of climatic, geologic and ecological processes as catalysts of diversification of the regions unique biota. Rather, recent work has shown that both biological and physical drivers of diversification are best analysed in a case‐by‐case setting with attention focused on the ecological and life‐history requirements of the specific phylogenetic lineage under investigation. Here, we utilize a comprehensive analytical approach to examine evolutionary drivers and elucidate the biogeographic history of Malagasy plated lizards (Zonosaurinae). Data from three genes are combined with fossil information to construct time‐calibrated species trees for zonosaurines and their African relatives, which are used to test alternative diversification hypotheses. Methods are utilized for explicitly incorporating phylogenetic uncertainty into downstream analyses. Species distribution models are created for 14 of 19 currently recognized species, which are then used to estimate spatial patterns of species richness and endemicity. Spatially explicit analyses are employed to correlate patterns of diversity with both topographic heterogeneity and climatic stability through geologic time. We then use inferred geographic ranges to estimate the biogeographic history of zonosaurines within each of Madagascars major biomes. Results suggest constant Neogene and Quaternary speciation with divergence from the African most recent common ancestor ~30 million years ago when oceanic currents and African rivers facilitated dispersal. Spatial patterns of diversity appear concentrated along coastal regions of northern and southern Madagascar. We find no relationship between either topographic heterogeneity or climatic stability and patterns of diversity. Ancestral state reconstructions suggest that western dry forests were important centres of origin with recent invasion into spiny and rain forest. These data highlight the power of combining multilocus phylogenetic and spatially explicit analyses for testing alternative diversification hypotheses within Madagascars unique biota and more generally, particularly as applied to phylogenetically and biologically constrained systems.

Habitat Use and Diet of Astrochelys radiata in the Subarid Zone of Southern Madagascar

Abstract Astrochelys radiata is one of the threatened tortoise species of Madagascar. We studied their home range size, use of shelters, and diet in Tsimanampetsotsa National Park. The goal was to identify suitable habitats and food chemistry. These data could serve as bases for future evaluations of the suitability of habitats under altered environmental conditions, such as degradation and climate change. The study was performed with the help of radio-tracking in two different types of vegetation: dry deciduous forest on sand and spiny bush on limestone between November 2007 and October 2008. Monthly range sizes were 2.3 ha in the littoral forest and 1.4 ha on the limestone massif when calculated with the kernel method. Based on the minimum convex polygon, the values were 1.0 and 0.5 ha, respectively. Monthly range size did not vary significantly between sexes, but range sizes were larger in the littoral forest than on limestone. A. radiata chose shelters under trees with large trunk diameters (> 15-cm DBH) and lower heights than trees in representative samples in the habitats. Plant items eaten and not eaten by this species were analyzed for primary and secondary plant chemicals. A. radiata consumed a wide variety of plants. Its diet was composed of leaves (91%), flowers (5%), and fruits (4%) from 109 plant species. During the dry season, high energy content was the most important factor for food selection by A. radiata.

Phylogeography of the arid-adapted Malagasy bullfrog, Laliostoma labrosum, influenced by past connectivity and habitat stability.

The rainforest biome of eastern Madagascar is renowned for its extraordinary biodiversity and restricted distribution ranges of many species, whereas the arid western region of the island is relatively species poor. We provide insight into the biogeography of western Madagascar by analyzing a multilocus phylogeographic dataset assembled for an amphibian, the widespread Malagasy bullfrog, Laliostoma labrosum. We find no cryptic species in L. labrosum (maximum 1.1% pairwise genetic distance between individuals in the 16S rRNA gene) attributable to considerable gene flow at the regional level as shown by genetic admixture in both mtDNA and three nuclear loci, especially in central Madagascar. Low breeding site fidelity, viewed as an adaptation to the unreliability of standing pools of freshwater in dry and seasonal environments, and a ubiquitous distribution within its range may underlie overall low genetic differentiation. Moreover, reductions in population size associated with periods of high aridity in western Madagascar may have purged DNA variation in this species. The mtDNA gene tree revealed seven major phylogroups within this species, five of which show mostly non-overlapping distributions. The nested positions of the northern and central mtDNA phylogroups imply a southwestern origin for all extant mtDNA lineages in L. labrosum. The current phylogeography of this species and paleo-distributions of major mtDNA lineages suggest five potential refugia in northern, western and southwestern Madagascar, likely the result of Pleistocene range fragmentation during drier and cooler climates. Lineage sorting in mtDNA and nuclear loci highlighted a main phylogeographic break between populations north and south of the Sambirano region, suggesting a role of the coastal Sambirano rainforest as a barrier to gene flow. Paleo-species distribution models and dispersal networks suggest that the persistence of some refugial populations was mainly determined by high population connectivity through space and time.