Mitochondrial evidence for distinct phylogeographic units in the endangered Malagasy poison frog Mantella bernhardi

The phylogeographic history of Megistostegium (Malvaceae) in the dry, spiny thickets of southwestern Madagascar using RAD-seq data and ecological niche modeling

The spiny thicket of southwestern Madagascar represents an extreme and ancient landscape with extraordinary levels of biodiversity and endemism. Few hypotheses exist for explaining speciation in the region and few plant studies have explored hypotheses for species diversification. Here, we investigate three species in the endemic genus Megistostegium (Malvaceae) to evaluate phylogeographic structure and explore the roles of climate, soil, and paleoclimate oscillations on population divergence and speciation throughout the region. We combine phylogenetic and phylogeographic inference of RADseq data with ecological niche modeling across space and time. Population structure is concurrent with major rivers in the region and we identify a new, potentially important biogeographic break coincident with several landscape features. Our data further suggests that niches occupied by species and populations differ substantially across their distribution. Paleodistribution modeling provide evidence that past climatic change could be responsible for the current distribution, population structure, and maintenance of species in Megistostegium.

Hidden in plain sight: a new frog species of the genus Blommersia from the oceanic island of Mayotte, Comoros archipelago

The amphibian fauna of the western Indian ocean volcanic island of Mayotte is currently constituted by two species belonging to two genera of the anuran family Mantellidae: Blommersia transmarina and Boophis nauticus. These were recently described after intense fieldwork on the herpetofauna of the island. We here describe a third new species of frog from Mayotte, based on morphological and molecular data, that occurs in sympatry with the others and was utterly unnoticed until now. Genetic analyses of the16S rRNA gene, including all described and several undescribed species of the genus Blommersia from Madagascar and Mayotte, confirms that the new species is the sister species of Blommersia transmarina. Both species show apparent morphological differences as well as different life histories, ecology and genetics that confirm Blommersia nataliae sp. nov. as a new species. We propose an IUCN Red List status of Critically Endangered for B. nataliae sp. nov.

Anthropogenic pressures drive population genetic structuring across a Critically Endangered lemur species range

In recent decades Madagascar has experienced significant habitat loss and modification, with minimal understanding of how human land use practices have impacted the evolution of its flora and fauna. In light of ongoing and intensifying anthropogenic pressures, we seek new insight into mechanisms driving genetic variability on this island, using a Critically Endangered lemur species, the black-and-white ruffed lemur (Varecia variegata), as a test case. Here, we examine the relative influence of natural and anthropogenic landscape features that we predict will impose barriers to dispersal and promote genetic structuring across the species range. Using circuit theory, we model functional connectivity among 18 sampling localities using population-based genetic distance (FST). We optimized resistance surfaces using genetic algorithms and assessed their performance using maximum-likelihood population-effects mixed models. The best supported resistance model was a composite surface that included two anthropogenic features, habitat cover and distance to villages, suggesting that rapid land cover modification by humans has driven change in the genetic structure of wild lemurs. Primary conservation priority should be placed on mitigating further forest loss and connecting regions identified as having low dispersal potential to prevent further loss of genetic diversity and promote the survival of other moist forest specialists.

Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella

Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantellamadagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantellaaurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantellacrocea + Mantellamilotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes.

Caught in the act: Incipient speciation across a latitudinal gradient in a semifossorial mammal from Madagascar, the mole tenrec Oryzorictes hova (Tenrecidae)

Madagascar is one of the world's foremost biodiversity hotspots, yet a large portion of its flora and fauna remains undescribed and the driving forces of in situ diversification are not well understood. Recent studies have identified a widespread, latitudinally structured phylogeographic pattern in Madagascar's humid-forest mammals, amphibians, reptiles, and insects. Several factors may be driving this pattern, namely biogeographic barriers (i.e., rivers or valleys) or past episodes of forest contraction and expansion. In this study, we describe the phylogeographic structure of the small, semifossorial mammal Oryzorictes hova, one of Madagascar's two species of mole tenrec, found throughout Madagascar's eastern humid forest belt, from high-elevation montane forest to low-elevation forests, as well as disturbed habitat such as rice fields. Using one mitochondrial locus, four nuclear loci, and 31 craniomandibular measurements, we identified three distinct populations of O. hova associated with the northern, central, and southern regions of the island. We found little evidence of gene flow among these populations, so we treated each population as a potential species. We validated species limits using two Bayesian methods: BP&P, employing only DNA sequence data, and iBPP using both DNA and morphological data, and we assessed whether these methods are susceptible to producing false positive errors. Molecular and morphological data support the recognition of each of the three populations of O. hova as distinct species, but formal species descriptions will require additional data from type specimens. This study illustrates the importance of using integrative datasets, multiple methodological approaches, and extensive geographic sampling for species delimitation and adds evidence for a widespread phylogeographic pattern in Madagascar's humid forest taxa.

Individual and Geographic Variation of Skin Alkaloids in Three Swamp-Forest Species of Madagascan Poison Frogs (Mantella)

Seventy skins of three mantellid frog species from Madagascan swamp-forest habitats, Mantella aurantiaca, M. crocea, and M. milotympanum, were individually examined for skin alkaloids using GC/MS. These poison frogs were found to differ significantly in their alkaloid composition from species of Mantella originating from non-flooded rainforest in eastern Madagascar, which were examined in earlier work. Only 16 of the previously detected 106 alkaloids were represented among the 60 alkaloids from the swamp-forest frogs of the present study. We hypothesize this difference is related mainly to habitat but cannot exclude a phylogenetic component as the three swamp-forest species are a closely related monophyletic group. The paucity of alkaloids with unbranched-carbon skeletons (ant-derived) and the commonness of alkaloids with branched-carbon skeletons (mite-derived) indicate that oribatid mites are a major source of alkaloids in these species of mantellids. Furthermore, most of the alkaloids have an oxygen atom in their formulae. Differences in alkaloids were observed among species, populations of the same species, and habitats. In M. aurantiaca, small geographic distances among populations were associated with differences in alkaloid profiles, with a remote third site illustrating even greater differences. The present study and an earlier study of three other mantellid species suggest that oribatid mites, and not ants, are the major source of alkaloids in the species of mantellids examined thus far.

Potential merger of ancient lineages in a passerine bird discovered based on evidence from host-specific ectoparasites

The merger of formerly isolated lineages is hypothesized to occur in vertebrates under certain conditions. However, despite many demonstrated instances of introgression between taxa in secondary contact, examples of lineage mergers are rare. Preliminary mtDNA sequencing of a Malagasy passerine, Xanthomixis zosterops (Passeriformes: Bernieridae), indicated a possible instance of merging lineages. We tested the hypothesis that X. zosterops lineages are merging by comparing mtDNA sequence and microsatellite data, as well as mtDNA sequence data from host-specific feather lice in the genus Myrsidea (Phthiraptera: Menoponidae). Xanthomixis zosterops comprises four deeply divergent, broadly sympatric, cryptic mtDNA clades that likely began diverging approximately 3.6 million years ago. Despite this level of divergence, the microsatellite data indicate that the X. zosterops mtDNA clades are virtually panmictic. Three major phylogroups of Myrsidea were found, supporting previous allopatry of the X. zosterops clades. In combination, the datasets from X. zosterops and its Myrsidea document a potential merger of previously allopatric lineages that likely date to the Pliocene. This represents the first report of sympatric apparent hybridization among more than two terrestrial vertebrate lineages. Further, the mtDNA phylogeographic pattern of X. zosterops, namely the syntopy of more than two deeply divergent cryptic clades, appears to be a novel scenario among vertebrates. We highlight the value of gathering multiple types of data in phylogeographic studies to contribute to the study of vertebrate speciation.

Sex-biased dispersal of a frog (Odorrana schmackeri) is affected by patch isolation and resource limitation in a fragmented landscape

Sex-biased dispersal is widespread in the animal kingdom and is affected by numerous factors including mating system, social factors and environmental conditions. Unlike birds and mammals, there is no common trend in amphibians and explaining the direction and degree of sex-biased dispersal in species-specific cases is difficult. We conducted a study on dispersal of the Chinese piebald odorous frog (Odorrana schmackeri) in a fragmented landscape associated with dam construction. Ten microsatellite loci were used to analyze 382 samples sourced from 14 fragmented ‘islands’. Assignment tests indicated a significant pattern of female-biased dispersal on one island with inconsistencies in the strength and direction of this pattern between nearby islands. The effects of four island attributes and two potential impact factors on the pattern of sex-biased dispersal were examined. We found that the extent of isolation from the mainland and the number of breeding sites both showed a negative correlation with female biased dispersal, such that the closer an island is to the mainland the more likely it is to display female biased dispersal, and the more breeding sites on an island the more male immigrants. Based on these results, we conclude that geographic isolation and limited breeding resources are the most likely explanation for the patterns of dispersal observed in this fragmented population of amphibians.

Phylogeography of the malagasy ring-tailed mongoose, Galidia elegans, from mtDNA sequence analysis

The ring-tailed mongoose (Galidia elegans) represents one of the most widely distributed mongooses in Madagascar; however, we know little about the ecology of this seemingly ubiquitous species. Currently, G. elegans is divided into three recognized subspecies--G. e. elegans, G. e. dambrensis, and G. e. occidentalis--based on differences in pelage coloration between the distinct geographic locations. We used intraspecific DNA variation to describe the phylogenetic relationships among the described subspecies. Approximately 550 base pairs of the mitochondrial DNA control region were analyzed from 19 G. elegans specimens representing all three subspecies sampled from across the species' geographic range. Sequence data from outgroup taxa were included for comparison. Examination of the recovered sequences revealed a strongly supported distinct genetic signature in the western region of the island, but remained inconclusive with respect to supporting the designation of the northern and eastern 'subspecies' for treatment as divergent intraspecific units for management.

Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles

Using sequences of the mitochondrial 16S rRNA gene, we reconstructed the phylogeography of six widely distributed Malagasy reptiles: two gekkonid lizard species, Phelsuma lineata and Hemidactylus mercatorius; two chameleons, the Calumma brevicorne complex, and Furcifer lateralis; and two skinks, Trachylepis gravenhorstii and Trachylepis elegans. Genetic differentiation among major haplotype lineages was high and in some cases indicates or confirms species status of the divergent populations. Maximum uncorrected sequence divergences were between 2.2% and 8.3% within the various species or species complexes. Haplotype lineages were exclusive to geographic regions, except in the commensal H. mercatorius where in three anthropogenic habitats coexistence of haplotype lineages was observed, possibly due to human translocation. The eastward flowing rivers Mangoro and Mananara may represent barriers to gene flow in the case of three species each. Some species sampled from humid eastern and arid western Madagascar showed no differentiation between populations from these two regions; instead the pattern observed was in several cases more concordant with a differentiation along a north-south axis.

Evidence for recent gene flow between north-eastern and south-eastern Madagascan poison frogs from a phylogeography of the Mantella cowani group

Background

The genus Mantella, endemic poison frogs of Madagascar with 16 described species, are known in the field of international pet trade and entered under the CITES control for the last four years. The phylogeny and phylogeography of this genus have been recently subject of study for conservation purposes. Here we report on the studies of the phylogeography of the Mantella cowani group using a fragment of 453 bp of the mitochondrial cytochrome b gene from 195 individuals from 21 localities. This group is represented by five forms: M. cowani, a critically endangered species, a vulnerable species, M. haraldmeieri, and the non-threatened M. baroni, M. aff. baroni, and M. nigricans.

Results

The Bayesian phylogenetic and haplotype network analyses revealed the presence of three separated haplotype clades: (1) M. baroni, M. aff. baroni, M. nigricans, and putative hybrids of M. cowani and M. baroni, (2) M. cowani and putative hybrids of M. cowani and M. baroni, and (3) M. haraldmeieri. The putative hybrids were collected from sites where M. cowani and M. baroni live in sympatry.

Conclusion

These results suggest (a) a probable hybridization between M. cowani and M. baroni, (b) a lack of genetic differentiation between M. baroni/M. aff. baroni and M. nigricans, (c) evidence of recent gene-flow between the northern (M. nigricans), eastern (M. baroni), and south-eastern (M. aff. baroni) forms of distinct coloration, and (d) the existence of at least three units for conservation in the Mantella cowani group.