Characterization of 20 microsatellite marker loci in Coquerel's sifaka (Propithecus coquereli)

The Coquerel's sifaka (Propithecus coquereli) is one of the species of Propithecus, living in the dry forest of northwest Madagascar. This species is endangered due to the loss and fragmentation of its natural habitat, consequential of deforestation. Twenty nuclear microsatellite loci were isolated from genomic DNA derived from a free ranging Coquerel's sifaka from the Mariarano Classified Forest, Madagascar. Population genetic parameters were estimated as baseline values from samples collected in that forest.     

Characterization of polymorphic microsatellite markers for the endangered Malagasy radiated tortoise (Geochelone radiata)

The radiated tortoise (Geochelone radiata) is an endangered endemic species from Madagascar that inhabits the semiarid spiny forest of the southern part of the island. Habitat destruction and illegal harvesting greatly threaten this species, as attested by the significant reduction of its distribution area in the past 30 years. In order to undertake appropriate conservation actions, it is essential to acquire a better knowledge of its genetic structure. For this study, 145 blood samples were collected from three populations of radiated tortoises in southwestern Madagascar. Eight microsatellite loci were found to be polymorphic, and allelic diversity and observed heterozygosity were high for all markers.     

Climate change and human colonization triggered habitat loss and fragmentation in Madagascar

The relative effect of past climate fluctuations and anthropogenic activities on current biome distribution is subject to increasing attention, notably in biodiversity hot spots. In Madagascar, where humans arrived in the last ~4 to 5,000 years, the exact causes of the demise of large vertebrates that cohabited with humans are yet unclear. The prevailing narrative holds that Madagascar was covered with forest before human arrival and that the expansion of grasslands was the result of human‐driven deforestation. However, recent studies have shown that vegetation and fauna structure substantially fluctuated during the Holocene. Here, we study the Holocene history of habitat fragmentation in the north of Madagascar using a population genetics approach. To do so, we infer the demographic history of two northern Madagascar neighbouring, congeneric and critically endangered forest dwelling lemur species—Propithecus tattersalli and Propithecus perrieri—using population genetic analyses. Our results highlight the necessity to consider population structure and changes in connectivity in demographic history inferences. We show that both species underwent demographic fluctuations which most likely occurred after the mid‐Holocene transition. While mid‐Holocene climate change probably triggered major demographic changes in the two lemur species range and connectivity, human settlements that expanded over the last four millennia in northern Madagascar likely played a role in the loss and fragmentation of the forest cover.     

The importance of littoral forest remnants for indigenous bird conservation in southeastern Madagascar

The littoral forests of Madagascar are relatively unexplored ecosystems that are considered seriously threatened by deforestation and habitat fragmentation. We set out to describe the bird communities inhabiting the littoral forest remnants in three different sub-regions of southeastern Madagascar to determine the national importance of these forests for bird conservation. In total, 77 bird species were found inhabiting 14 littoral forest remnants. Of these species, 40 are endemic to Madagascar and a further 21 are endemic to the Indian Ocean sub-region, consisting of Madagascar, the Comoros and the Mascarenes. The matrix habitats (Melaleuca forests, marécage swamp forest, Eucalyptus plantations and Erica grassland) that immediately surround the littoral forests were depauperate of bird species and contained few species that were found within the littoral forests. The geographic location of littoral forest remnants had an important role in determining what bird species occurred within them, with the northern remnants having similar bird communities to nearby humid forest whilst the most southern remnant had a bird community that resembled those of nearby spiny forest habitats. Eleven bird species that have been previously described as being habitat-restricted endemics to either spiny forests or humid forests, were found in littoral forest remnants. These results suggest that these littoral forests may play an important transitional role between the two other major natural habitats (spiny forest and humid forest) of southeastern Madagascar. On this basis we advocate that the littoral forest remnants of southeastern Madagascar should be afforded continuing conservation priority.     

Current geographical ranges of Malagasy dung beetles are not delimited by large rivers

Aim We investigated whether the largest river (Mangoro) on the east coast of Madagascar acts as a barrier to dispersal in dung beetles by comparing species composition and genetic differentiation of the most common species on the two banks of the river. Moreover, by analysing the current geographical ranges of all wet forest dung beetle species, possible long‐term effects of the largest rivers on the distribution of species were assessed. Location Madagascar. Methods Dung beetles were sampled with baited pitfall traps at a downstream and an upstream locality on the two banks of the Mangoro River. The most common species, Nanos binotatus (Canthonini), was sequenced for cytochrome c oxidase subunit I (COI; 804 bp) to characterize within‐population diversity and between‐population genetic differentiation. For the analysis of species geographical range boundaries in relation to the position of the largest rivers on the east coast, a database including all the records for 158 wet forest species was used. The congruence of species range boundaries with the positions of the rivers was tested with a randomization test. Results All common species were found on both sides of the Mangoro River. In Nanos binotatus, haplotype and nucleotide diversities ranged from 0.25 to 0.85 and 0.001 to 0.01, respectively. Population differentiation was high and significant in all comparisons (P < 0.01; average F_ST = 0.61). The differentiation was not significantly higher across than along the river, as would be expected by the riverine barrier hypothesis. There was no indication that the range boundaries of wet forest dung beetle species would generally coincide with the largest rivers in eastern Madagascar. Main conclusions The results provide little support for the riverine barrier hypothesis as an explanation for the current range boundaries of dung beetles in eastern Madagascar. However, extensive deforestation of the coastal regions in eastern Madagascar may have caused a great shrinkage of the ranges of many forest‐dwelling species. Thus the present‐day distributions may not reflect accurately the patterns of the past geographical ranges of the species.     

Extending ecological niche models to the past 120 000 years corroborates the lack of strong phylogeographic structure in the Crested Drongo (Dicrurus forficatus forficatus) on Madagascar

We conduct a phylogeographic study of the Crested Drongo (Dicrurus forficatus forficatus), a broadly distributed bird species on Madagascar. We first determined the demographic and spatial pattern inferred from mitochondrial and nuclear data, and then compared these results with predictions from a present to 0.120‐Myr‐old reconstruction of the spatial dynamics of the range of D. f. forficatus on Madagascar, enabling putative areas of stability (lineage persistence) to be detected. Weak genetic structure along an east–west pattern and comparatively low genetic diversity were recovered, with strong evidence of population expansion found at all ten loci sampled. The palaeoclimatic distribution models over the past 0.120 Myr suggest the presence of extensive areas of suitable climate in the east and west for the species since its colonization of Madagascar, a result in strong concordance with the spatial and genetic signal derived from our multilocus data set. © 2013 The Linnean Society of London     

Contrasting genetic diversity and population structure among three sympatric Madagascan shorebirds: parallels with rarity,endemism, and dispersal

Understanding the relative contributions of intrinsic and extrinsic factors to population structure and genetic diversity is a central goal of conservation and evolutionary genetics. One way to achieve this is through comparative population genetic analysis of sympatric sister taxa, which allows evaluation of intrinsic factors such as population demography and life history while controlling for phylogenetic relatedness and geography. We used ten conserved microsatellites to explore the population structure and genetic diversity of three sympatric and closely related plover species in southwestern Madagascar: Kittlitz's plover (Charadrius pecuarius), white‐fronted plover (C. marginatus), and Madagascar plover (C. thoracicus). Bayesian clustering revealed strong population structure in the rare and endemic Madagascar plover, intermediate population structure in the white‐fronted plover, and no detectable population structure in the geographically widespread Kittlitz's plover. In contrast, allelic richness and heterozygosity were highest for the Kittlitz's plover, intermediate for the white‐fronted plover and lowest for the Madagascar plover. No evidence was found in support of the “watershed mechanism” proposed to facilitate vicariant divergence of Madagascan lemurs and reptiles, which we attribute to the vagility of birds. However, we found a significant pattern of genetic isolation by distance among populations of the Madagascar plover, but not for the other two species. These findings suggest that interspecific variation in rarity, endemism, and dispersal propensity may influence genetic structure and diversity, even in highly vagile species.     

Long-term genetic monitoring of a translocated population of collared brown lemurs

Post-release monitoring is important to improve translocation success because it provides an opportunity to identify factors relevant to the survival of local populations. We studied a population of the endangered collared brown lemur (Eulemur collaris) translocated from a degraded forest fragment to a nearby littoral forest within the Mandena Conservation Area in southeast Madagascar from 2000–2011. We compared genetic surveys of mitochondrial and nuclear markers with the genetic profile of nearby populations to examine the dispersal capacity of the collared brown lemur. We also performed a landscape analysis to assess changes in connectivity between forest fragments. There was a fluctuating trend characterized by a phase of demographic and genetic stability shortly after translocation, followed by an increase in genetic diversity coinciding with a population decrease and a gradual recovery of initial conditions. These results demonstrated the ability of the collared brown lemur to disperse through unfavorable landscapes and to recover after translocation. Our study revealed the importance of monitoring translocated populations over time using a multidisciplinary approach.     

Characterization of 20 microsatellites marker loci in the golden-crowned sifaka (<Emphasis Type="Italic">Propithecus tattersalli)</Emphasis>

The golden-crowned sifaka (Propithecus tattersalli) is one of the most critically endangered species of Propithecus endemic to a limited area in the Daraina region of north-eastern Madagascar. This species is endangered due to habitat loss and fragmentation, a consequence of deforestation. Twenty nuclear microsatellite loci were isolated from genomic DNA derived from a Propithecus tattersalli from the Daraina area in north-eastern Madagascar. Population genetic parameters were estimated on 20 individuals from two Daraina forest fragments to determine the potential utility of this marker suite for future studies on the golden-crowned sifaka.     

The effect of deforestation on the genetic diversity and structure in <Emphasis Type="Italic">Acer saccharum</Emphasis> (Marsh): Evidence for the loss and restructuring of genetic variation in a natural system

The level and distribution of genetic diversity can be influenced by species life history traits and demographic factors, including perturbations that might produce population bottlenecks. Deforestation and forest fragmentation are common sources of population disturbance in contemporary populations of forest ecosystems. Although the genetic effects of forest fragmentation and deforestation have been examined by assessing levels of genetic variation in forest fragments that remain after logging, few considerations have been made of the populations that re-colonize once-cleared areas. Here we examine the effects of human-mediated population bottlenecks on the level and distribution of genetic diversity in natural populations of the long-lived forest tree species, Acer saccharum (sugar maple). We compared genetic variation and structure for populations of sugar maple found within old-growth forested area and in area that has re-colonized since logging. In this study the percent polymorphic loci and allelic richness estimates were reduced in the logged populations compared to old-growth populations. Jackknifed estimates of population genetic differentiation showed significantly higher differentiation among logged populations, with this result being consistently seen when individuals within populations were grouped according to diameter at breast height. The result of decreased genetic variation and higher levels of genetic structure among logged populations suggests that even one extensive bout of logging can alter the level and distribution of genetic variation in this forest tree species.     

Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents

This study is the first large‐scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4–26°S and 33–48°E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D_EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale—across national borders.     

Genetically and geographically isolated lineages of a tropical bat (Chiroptera: Molossidae) show demographic stability over the late Pleistocene

The newly described molossid bat, Chaerephon atsinanana Goodman et al., 2010, endemic to eastern Madagascar, shows notably high levels of phylogeographic and genetic structure compared with allopatric Chaerephon leucogaster Grandidier, 1869 from western Madagascar. Such highly significant structuring of haplotypes among altitudinally and latitudinally stratified population groups is contrary to the expected panmixia in strong flying bats. The null model of concordance in historical demographic patterns across these two Chaerephon species was not supported. Mismatch and Bayesian skyline analyses indicated ancient stable C. atsinanana populations of constant size during the last two major Pleistocene glacial periods, making retreat into and expansion from glacial refugia an unlikely explanation for such high levels of structure, in accordance with expectations for tropical bats. Analyses were consistent with post‐refugial population expansion in the less diverse and structured C. leucogaster during the end of the last Pleistocene glacial period. We hypothesise that the pronounced genetic structuring in C. atsinanana may result from female philopatry. Furthermore, differing demographic histories of the two species may have been shaped by differing climate or habitat preferences, consistent with evidence from MaxEnt ecological niche modelling, which shows differences in variables influencing the current predicted distributions. Fossil Quaternary pollen deposits further indicate greater stability in past climatic patterns in eastern versus western Madagascar. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 18–40.     

Linking seed dispersal and genetic structure of trees: a biogeographical approach

Aim Natural and human‐induced differences in frugivore assemblages can influence the seed dispersal distances of trees. An important issue in seed dispersal systems is to understand whether differences in seed dispersal distances also affect the genetic structure of mature trees. One possible approach to test for a relationship between seed dispersal and the genetic structure of mature trees is to compare the genetic structure of two closely related tree species between two biogeographical regions that differ in frugivore assemblages and seed dispersal distances. Previous studies on two Commiphora species revealed that Commiphora guillauminii in Madagascar has a much lower seed dispersal distance than Commiphora harveyi in South Africa. We tested whether the lower seed dispersal distance might have caused decreased gene flow, resulting in a stronger genetic structure in Madagascar than in South Africa. Location Madagascar and South Africa. Methods Using amplified fragment length polymorphism markers we investigated the genetic structure of 134 trees in Madagascar and 158 trees in South Africa at a local and a regional spatial scale. Results In concordance with our hypothesis, kinship analysis suggests that gene flow was restricted mostly to 3 km in Madagascar and to 30 km in South Africa. At the local spatial scale, the genetic differentiation among groups of trees within sample sites was marginally significantly higher in Madagascar (F_ST = 0.069) than in South Africa (F_ST = 0.021). However, at a regional spatial scale genetic differentiation was lower in Madagascar (F_ST = 0.053) than in South Africa (F_ST = 0.163). Main conclusions Our results show that lower seed dispersal distances of trees were linked to higher genetic differentiation of trees only at a local spatial scale. This suggests that seed dispersal affects the genetic population structure of trees at a local, but not at a regional, spatial scale.     

Characterization of 21 microsatellite marker loci in the ring-tailed lemur (<Emphasis Type="Italic">Lemur catta</Emphasis>)

Ring-tailed lemur (Lemur catta) is the only species in the Genus Lemur, distributed in the deciduous and spiny forests of southwestern Madagascar. This species is listed as endangered due to the loss and fragmentation of its natural habitat, a consequence of deforestation. Twenty-one nuclear microsatellite loci were isolated from a genomic DNA derived from a free-ranging ring-tailed lemur population from the Tsimanampetsotsa National Park, Madagascar. We report various parameter estimates and measures to establish the utility of this marker suite as screened among individuals this single forest fragment.     

Characterization of 13 microsatellite marker loci in Verreaux's sifaka (Propithecus verreauxi)

The Verreaux's sifaka (Propithecus verreauxi) is one of the species of Propithecus, living in the dry forest of southwest Madagascar. This species is endangered due to the loss and fragmentation of its natural habitat, a consequence of deforestation. Thirteen novel nuclear microsatellite loci were isolated and characterized in three populations of Verreaux's sifaka. The marker suite proved informative with an average of 8.9 alleles per locus and observed heterozygosity across the three populations of 0.675.     

Biogeography of Dwarf Lemurs: Genetic Evidence for Unexpected Patterns in Southeastern Madagascar

Seven species of dwarf lemurs (Cheirogaleus spp.) are currently recognized after a recent revision of the genus. During a field study in southeastern Madagascar, we observed 3 distinct morphotypes of Cheirogaleus resembling Cheirogaleus medius, C. major and C. crossleyi. In particular, for Cheirogaleus crossleyi southeastern Madagascar was far away from the known distribution range of the species when referring to the recent revision of the genus. In order to clarify the taxonomic status of the 3 morphotypes, we compared field samples from southeastern Madagascar to museum specimens from several locations in Madagascar and to field samples from Kirindy/CFPF, western Madagascar by genetic analyses using the mitochondrial cytochrome b gene. Genetic data yield strong support for 2 of the 3 morphotypes to represent Cheirogaleus medius and C. major. The third morphotype is genetically closely related to Cheirogaleus crossleyi, albeit more distantly than the other 2 morphotypes to the respective reference samples. The genetic distance is related to a considerable geographic distance between the location of our field study and the origin of the respective reference specimen, because Cheirogaleus crossleyi had been reported only from northern Madagascar. Our field observations indicate an isolated population in southeastern Madagascar. We propose to identify them as Cheirogaleus crossleyi and discuss the population genetic and biogeographic considerations supporting this conclusion.     

Genetic structure of Helianthus occidentalis (Asteraceae) in a preserve withfragmented habitat

We examined the spatial genetic structure of Helianthus occidentalis Riddell ssp. occidentalis Riddell (western sunflower) to determine whether this species is highly clonal and whether the distance between prairie patches influences genetic differentiation. In the Edge of Appalachia Preserve System, Ohio, this species is restricted to prairie patches that have a clumped distribution in the forest matrix. Data from this insect-pollinated forb with gravity-dispersed seed were compared to data from the same patches for Asclepias verticillata, an insect-pollinated species with wind-dispersed seed. Allozyme electrophoresis was used to collect genetic data from H. occidentalis samples from eight patches in four regions. Genetic data from three polymorphic loci indicted that this species is not highly clonal. Genetic differentiation was greater among patches within a region than among regions, suggesting that gene flow among patches is more limited in H. occidentalis than in A. verticillata. Founder effect may also have contributed to observed genetic differences among patches as some of these populations may have re-established after release from human use. As habitat fragmentation is increasing in the preserve, it is also likely that genetic differentiation may be increasing. Therefore, monitoring of genetic structure is necessary to further assess the effect of fragmentation.     

<Emphasis Type="Italic">Oliganthes anjanaribensis,</Emphasis> a new species of Compositae: Vernonieae from Madagascar

Oliganthes anjanaribensis Beentje & D. J. N. Hind (Compositae: Vernonieae), a forest shrub from a protected area in NE Madagascar, is described and illustrated. Both species and genus are endemic to Madagascar. The conservation status of the species is briefly discussed.     

Latitude drives diversification in Madagascar's endemic dry forest rodent Eliurus myoxinus (subfamily Nesomyinae)

Numerous hypotheses have been proposed for the historical processes governing the rich endemism of Madagascar's biodiversity. The ‘watershed model’ suggests that drier climates in the recent geological past have resulted in the contraction of forests around major watersheds, thereby defining areas of endemism. We test whether this hypothesis explains phylogeographical patterns in a dry forest‐dependent rodent, Eliurus myoxinus, an endemic species widely distributed through western Madagascar. We sequenced the mitochondrial cytochrome b locus and nuclear introns of the β‐fibrinogen and the growth hormone receptor genes for E. myoxinus. Using a parametric bootstrapping approach, we tested whether the mitochondrial gene tree data fit expectations of local differentiation given the watershed model. We additionally estimated population differentiation and historical demographic parameters, and reconstructed the spatial history of E. myoxinus to highlight spatial and temporal patterns of differentiation. The data do not support the watershed model as a clear explanation for the genetic patterns of diversity within extant E. myoxinus populations. We find striking patterns of latitudinal genetic structure within western Madagascar, and indicate possible roles for environmental and ecological gradients along this axis in generating phylogeographical diversity. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 500–517.     

Divergent sympatric lineages of the Atlantic and Indian Ocean crinoid Tropiometra carinata

The shallow water comatulid crinoid Tropiometra carinata is native to both the Atlantic and Indian Oceans, a distribution anomalous among shallow water crinoids and many other broadcast spawning species. Given this species' short pelagic larval duration, the findings of previous work that suggest that the Benguela upwelling is a significant barrier to gene flow in broadcast spawning species, and T. carinata's unexpected geographic distribution, we predicted that the crinoids presently recognized as T. carinata consisted of a species complex. To test this prediction, we sequenced a portion of the mitochondrial cytochrome oxidase 1 gene from 30 individuals of T. carinata collected from Brazil, the Mozambique Channel, Madagascar, and Reunion Island. We found that nucleotide divergence ranged 0.02–3.10% among haplotypes. Moreover, while a Bayesian phylogenetic tree indicated that there were two substantially divergent genetic lineages, there was no evidence to support that T. carinata is comprised of a species complex due to isolation‐by‐distance. Surprisingly, both lineages were found in sympatry in both the Atlantic and Indian Oceans. Likewise, a 95% parsimony haplotype network revealed that identical haplotypes are found in both oceans, suggesting that a species complex may indeed exist, just not one caused by geographic isolation. We discuss possible explanations for this unexpected genetic structure, such as natural dispersal or human‐mediated movement, and how the genetic structure found here is relevant to other marine organisms and to cryptic speciation.