Late Holocene spread of pastoralism coincides with endemic megafaunal extinction on Madagascar.

Recently expanded estimates for when humans arrived on Madagascar (up to approximately 10 000 years ago) highlight questions about the causes of the island's relatively late megafaunal extinctions (approximately 2000-500 years ago). Introduced domesticated animals could have contributed to extinctions, but the arrival times and past diets of exotic animals are poorly known. To conduct the first explicit test of the potential for competition between introduced livestock and extinct endemic megafauna in southern and western Madagascar, we generated new radiocarbon and stable carbon and nitrogen isotope data from the bone collagen of introduced ungulates (zebu cattle, ovicaprids and bushpigs, n = 66) and endemic megafauna (pygmy hippopotamuses, giant tortoises and elephant birds, n = 68), and combined these data with existing data from endemic megafauna (n = 282, including giant lemurs). Radiocarbon dates confirm that introduced and endemic herbivores briefly overlapped chronologically in this region between 1000 and 800 calibrated years before present (cal BP). Moreover, stable isotope data suggest that goats, tortoises and hippos had broadly similar diets or exploited similar habitats. These data support the potential for both direct and indirect forms of competition between introduced and endemic herbivores. We argue that competition with introduced herbivores, mediated by opportunistic hunting by humans and exacerbated by environmental change, contributed to the late extinction of endemic megafauna on Madagascar.

New evidence of megafaunal bone damage indicates late colonization of Madagascar.

The estimated period in which human colonization of Madagascar began has expanded recently to 5000-1000 y B.P., six times its range in 1990, prompting revised thinking about early migration sources, routes, maritime capability and environmental changes. Cited evidence of colonization age includes anthropogenic palaeoecological data 2500-2000 y B.P., megafaunal butchery marks 4200-1900 y B.P. and OSL dating to 4400 y B.P. of the Lakaton'i Anja occupation site. Using large samples of newly-excavated bone from sites in which megafaunal butchery was earlier dated >2000 y B.P. we find no butchery marks until ~1200 y B.P., with associated sedimentary and palynological data of initial human impact about the same time. Close analysis of the Lakaton'i Anja chronology suggests the site dates <1500 y B.P. Diverse evidence from bone damage, palaeoecology, genomic and linguistic history, archaeology, introduced biota and seafaring capability indicate initial human colonization of Madagascar 1350-1100 y B.P.

Genomic landscape of human diversity across Madagascar.

Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea).

The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.

Large rivers do not always act as species barriers for Lepilemur sp.

Sportive lemurs constitute a highly diverse endemic lemur family (24 species) for which many biogeographic boundaries are not yet clarified. Based on recent phylogeographic models, this study aims to determine the importance of two large rivers (the Antainambalana and Rantanabe) in northeastern Madagascar as species barriers for Lepilemur seali. The Antainambalana River was previously assumed to act as the southern border of its distribution. A total of 1,038 bp of the mtDNA of four individuals stemming from two adjacent inter-river systems south of the Antainambalana River was sequenced and compared to sequences of 22 described Lepilemur species. The phylogenetic reconstruction did not find support for either of the two rivers as species barrier for Lepilemur, as all captured individuals clustered closely with and therefore belonged to L. seali. However, a previously published sequence of an individual from a site south of our study sites belongs to a separate species. The southern boundary of L. seali must therefore be one of two large rivers further south of our study sites. The results suggest that L. seali may possess a relatively large altitudinal range that enabled this species to migrate around the headwaters of the Antainambalana and Rantanabe Rivers. Previous phylogeographic models need to be refined in order to incorporate these findings, and more species-specific altitudinal range data are urgently needed in order to fully understand the biogeographic patterns of lemurs on Madagascar.

Exceptional diversity of mouse lemurs (Microcebus spp.) in the Makira region with the description of one new species.

Although the number of described lemur species has increased considerably over the last 20 years, detailed biogeographic data are still lacking from many geographic regions, in particular in the eastern part of Madagascar. This study investigated mouse lemur species diversity in a previously unstudied Inter-River-System in the eastern Makira region. Three sites were visited and 26 individuals were sampled and characterized with 13 external morphometric measurements. Standard phylogenetic analyses were performed on the basis of sequences of three mitochondrial loci by including representatives of all other published mouse lemur species for comparison. The analyses revealed the presence of three mouse lemur species in one study site, two of which were previously undescribed. The two new species are genetically distinct and belong to the larger-bodied mouse lemur species on the island, whereas the third species, Microcebus mittermeieri, belongs to the smaller-bodied mouse lemur species. The study fully describes one of the new species. This study and other lemur inventories suggest that the Makira region is particularly rich in lemur species and the lack of any protected zone in this area should now attract the urgent attention of conservation stakeholders.