Lauren M. Chan

Relationships of the Salamandrid Genera Paramesotriton, Pachytriton, and Cynops Based on Mitochondrial DNA Sequences

Abstract We compared 786 base pairs of cytochrome b mitochondrial DNA sequence to examine the evolutionary relationships among seven species belonging to three genera of Asian newts: Paramesotriton, Pachytriton, and Cynops. We find strong evidence supporting recognition of a clade for these genera. Although bootstrap support values are relatively low, both parsimony and likelihood analyses suggest that the species of Paramesotriton sampled form a monophyletic group with Paramesotriton caudopunctatus basal to the other three species. Cynops appears to be paraphyletic, with Pachytriton and Paramesotriton being more closely related to Cynops pyrrhogaster than to Cynops cyanurus. Pachytriton and Paramesotriton exhibit some morphological similarities and have more specialized breeding habits and environmental requirements than Cynops, suggesting that they shared an evolutionary history before diverging. Our morphological investigations corroborate previous studies that suggested Cynops is the most generalized representative of the clade and that it retains several ancestral character states.

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.

Phylogeny and biogeography of western Indian Ocean Rousettus (Chiroptera: Pteropodidae)

Abstract We examined patterns of genetic variation in Rousettus madagascariensis from Madagascar and R. obliviosus from the Comoros (Grande Comore, Anjouan, and Mohéli). Genetic distances among individuals on the basis of 1,130 base pairs of the mitochondrial cytochrome b (Cytb) locus were estimated from specimens collected from 17 sites on Madagascar, 3 sites on Grande Comore, 3 sites on Anjouan, and 2 sites on Mohéli. We observed little variation in Madagascar and nearshore island samples (maximum 1.1%) and interisland Comoros samples (maximum 1.8%). In contrast, pairwise distances between different sampled sites on Madagascar and the Comoros varied from 8.5% to 13.2%. For 131 Malagasy animals, 69 unique haplotypes were recovered with 86 variable sites, and for 44 Comorian individuals, 17 unique haplotypes were found with 30 variable sites. No haplotype was shared between Madagascar and the Comoros, adding to previous morphological evidence that these 2 populations should be considered separate species. Cytb data showed that Rousettus populations of Madagascar (including nearshore islands) and the Comoros are respectively monophyletic and display no geographic structure in haplotype diversity, and that R. madagascariensis and R. obliviosus are strongly supported as sister to each other relative to other Rousettus species. Genotypic data from 6 microsatellite loci confirm lack of geographic structure in either of the 2 species. In pairwise tests of population differentiation, the only significant values were between samples from the Comoro Islands and Madagascar (including nearshore islands). Estimates of current and historical demographic parameters support population expansion in both the Comoros and Madagascar. These data suggest a more recent and rapid demographic expansion in Madagascar in comparison with greater population stability on the Comoros. On the basis of available evidence, open-water crossings approaching 300 km seem rarely traversed by Rousettus, and, if successful, can result in genetic isolation and subsequent differentiation.

Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates.

Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available.

Increased population sampling confirms low genetic divergence among Pteropus (Chiroptera: Pteropodidae) fruit bats of Madagascar and other western Indian Ocean islands

Fruit bats of the genus Pteropus occur throughout the Austral-Asian region west to islands off the eastern coast of Africa. Recent phylogenetic analyses of Pteropus from the western Indian Ocean found low sequence divergence and poor phylogenetic resolution among several morphologically defined species. We reexamine the phylogenetic relationships of these taxa by using multiple individuals per species. In addition, we estimate population genetic structure in two well-sampled taxa occurring on Madagascar and the Comoro Islands (P. rufus and P. seychellensis comorensis). Despite finding a similar pattern of low sequence divergence among species, increased sampling provides insight into the phylogeographic history of western Indian Ocean Pteropus, uncovering high levels of gene flow within species.

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.

Allotetraploids in Patagonia with Affinities to Western North American Diploids: Did Dispersal or Genome Doubling Occur First?

Amphitropical disjunct distributions between western North America and western South America have intrigued botanists for over a century. Here, specific examples of migration and speciation are investigated using herbaceous species from the phlox family (Polemoniaceae) as a model for considering the timing of dispersal relative to speciation. Comparative DNA sequencing reveals that, in Collomia and Navarretia, the South American species are allopolyploids, suggesting either two dispersals prior to the allopolyploidization event for each species with subsequent extirpation of the diploid progenitors from South America, or allopolyploid formation prior to dispersal with extirpation of these polyploids from North America. Divergence time estimates support a Pliestocene dispersal hypothesis and sequence data indicate that, at least in Collomia, hybridization of the diploid progenitors occurred in South America.ResumenLas distribuciones anfitropicales disyuntas entre el oeste de América del Norte y el oeste de América del Sur han intrigado a los botánicos durante más de un siglo. Aquí se investigan ejemplos específicos de migración y especiación usando especies de la familia del Flox (Polemoniaceae) como un modelo para considerar el efecto del orden temporal entre dispersión y especiación. La comparación de sequencias de ADN revela que las especies sudamericanas de Navarretia y Collomia son alopoliploides y sugiere para cada una de ellas, o bien dos eventos de dispersión anteriores a la formación del alopoliploide, seguido por la desaparición de los progenitores diploides en América del Sur, o bien la formación del alopoliploide antes de la dispersión, y la extinción de los progenitores diploides en América del Norte. La estimación de los tiempos de divergencia apoya la hipótesis de una dispersión durante el Pleistoceno, y los datos de las secuencias de ADN indican que, al menos en el caso de Collomia, la hibridación de los progenitores diploides ocurrió en América del Sur.

A Deep Divergence Time between Sister Species of Eidolon (Pteropodidae) with Evidence for Widespread Panmixia

The pteropodid fruit bat genus Eidolon is comprised of two extant species: E. dupreanum on Madagascar and E. helvum on the African mainland and offshore islands. Recent population genetic studies of E. helvum indicate widespread panmixia across the continent, although island populations off western Africa show genetic structure. Little is known about the genetic connectivity of E. dupreanum or the divergence time between these two sister species. We examine sequence data for one mitochondrial (cyt-b) and three nuclear regions (&bgr;-fib, RAG1, and RAG2) to assess population genetic structure within E. dupreanum and divergence between the two Eidolon spp. In addition, we characterize the demographic history of both taxa using coalescent-based methods. We find little evidence for population structure within E. dupreanum, and suggest that this reflects dispersal based on seasonal fruit availability and a preference for roosting sites in exposed rock outcrops. However, despite apparent panmixia in both Eidolon spp. and large dispersal distances reported in previous studies for E. helvum, these two taxa diverged in the mid-to-late Miocene. Both species are also characterized by population expansion and young, Pleistocene clade ages, although slower population growth in E. dupreanum is likely explained by its divergence via colonization from the mainland. Finally, we discuss the implications of population connectivity in E. dupreanum in the context of its potential role as a reservoir host for pathogens capable of infecting humans.

Does UV-B Radiation Affect Embryos of Three High Elevation Amphibian Species in California?

Abstract Declines and extinctions of amphibians in well-protected habitats suggest that global atmospheric factors may be responsible. We tested effects of field exposures of ultraviolet radiation (UV-B) on embryo hatching success and time to hatching in three anurans that inhabit high elevation areas of the Sierra Nevada in California, USA. While few obvious environmental impacts have occurred in the high elevation area of the Sierra Nevada, two of the three most common anurans, the Yosemite Toad (Bufo canorus) and the Southern Mountain Yellow-legged Frog (Rana muscosa), have suffered severe population declines while the sympatric Pacific Treefrog (Pseudacris regilla) has remained relatively abundant. Previous studies have shown that hatching of P. regilla embryos at lower elevations are not affected negatively by UV-B radiation. We hypothesized that differences in UV sensitivity may help explain why P. regilla remain abundant while B. canorus and R. muscosa have declined sharply. We conducted field experiments at two remote sites above 3030 m elevation over two years. No effect of UV-B was found on hatching success or rate of development in embryos of B. canorus, P. regilla, or R. muscosa, except for a small, context-dependent increase in time to hatching in R. muscosa. We recommend that research efforts on these species in the Sierra Nevada concentrate on post-hatching effects of UV-B, or on other decline hypotheses.