Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA.

Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia-Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.

Phylogeographic Analysis of Madagascan Goats Using mtDNA Control Region and SRY Gene Sequences.

In the present study, we estimated the genetic diversity and relationships, as well as the propagation routes, of Madagascan goats using mtDNA control region and SRY gene sequences. The mtDNA sequences of 40 Madagascan goats revealed 10 haplotypes and a quite low nucleotide diversity (0.0014), suggesting a founder and/or bottleneck effect resulting from goat migration to Madagascar island. The analysis of sequences identical to Madagascan haplotypes indicated close genetic relationships between goats from Madagascar and Africa. Sequence analysis of the SRY gene in 40 male Madagascan goats revealed two haplotypes: Y1A (45%) and Y2A (55%). The paternal result indicated genetic influences from Africa, South Asia, and the Near East proximal to Madagascar. The analyses of the mtDNA control region and SRY gene sequences suggested a genetic relationship between Africa and Madagascar. Moreover, SRY sequences indicated influences from South Asia and the Near East. These phylogenetic results provide important genetic information for elucidating the propagation routes of Madagascan goats.

Diversity of photoreceptor arrangements in nocturnal, cathemeral and diurnal Malagasy lemurs.

The lemurs of Madagascar (Primates: Lemuriformes) are a monophyletic group that has lived in isolation from other primates for about 50 million years. Lemurs have diversified into species with diverse daily activity patterns and correspondingly different visual adaptations. We assessed the arrangements of retinal cone and rod photoreceptors in six nocturnal, three cathemeral and two diurnal lemur species and quantified different parameters in six of the species. The analysis revealed lower cone densities and higher rod densities in the nocturnal than in the cathemeral and diurnal species. The photoreceptor densities in the diurnal Propithecus verreauxi indicate a less "diurnal" retina than found in other diurnal primates. Immunolabeling for cone opsins showed the presence of both middle-to-longwave sensitive (M/L) and shortwave sensitive (S) cones in most species, indicating at least dichromatic color vision. S cones were absent in Allocebus trichotis and Cheirogaleus medius, indicating cone monochromacy. In the Microcebus species, the S cones had an inverse topography with very low densities in the central retina and highest densities in the peripheral retina. The S cones in the other species and the M/L cones in all species had a conventional topography with peak densities in the central area. With the exception of the cathemeral Eulemur species, the eyes of all studied taxa, including the diurnal Propithecus, possessed a tapetum lucidum, a feature only found among nocturnal and crepuscular mammals.

Characterization of the Tree Holes Used by Lepilemur ruficaudatus in the Dry, Deciduous Forest of Kirindy Mitea National Park.

Knowledge of the key resources for a species is critical for developing an effective conservation strategy. Kirindy Mitea National Park is an important refuge for the red-tailed sportive lemur (Lepilemur ruficaudatus), a nocturnal folivorous lemur endemic to the dry deciduous forest of western Madagascar. Because L. ruficaudatus sleeps in tree holes during the day, sleeping trees may be an important resource for this species. Our goal was to characterize the sleeping sites used by L. ruficaudatus at the Ankoatsifaka Research Station in Kirindy Mitea National Park. In July and August 2012, tree characteristics were recorded for 60 L. ruficaudatus sleeping sites. Intact and alive trees, particularly Strychnos madagascariensis, were preferred by L. ruficaudatus. Sleeping holes were generally located in taller trees (median hole height = 4 m) and in trees with large girths (median = 20.5 cm). Greater protection from predators and thermal shifts may be provided by intact trees and concealed tree holes. Because tree characteristics can influence the presence and abundance of forest-living primates, the availability and characteristics of particular trees as potential sleeping shelters in a habitat must be taken into account in conservation strategies for L. ruficaudatus.

A quill vibrating mechanism for a sounding apparatus in the streaked tenrec (Hemicentetes semispinosus).

The streaked tenrec (Hemicentetes semispinosus) is equipped with a quill vibrating mechanism on the dorsal side of the caudal trunk that has evolved as an extraordinary sounding apparatus for communication. An arrangement of 15 or 16 light-brown quills was observed. Thickened cutaneous muscles were confirmed beneath quills. We named this structure the "quill vibrator disc" (QVD). The QVD was 16.8 mm long and 8.55 mm wide in a typical adult. Longitudinal musculature symmetrical about the sagittal plane was developed in the QVD. Myocytes were found immunohistochemically to contain mainly fast myosin but not slow myosin. These findings indicate that the QVD is a specialized apparatus in the cutaneous muscle that contributes to the vibration of quills and to the production of sound for communication.

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs.

Prosimians (tarsiers and strepsirrhini) represent the basal lineages in primates and have a close bearing on the origin of primates. Although major lineages among anthropoidea (humans, apes and monkeys) are well represented by complete mitochondrial DNA (mtDNA) sequence data, only one complete mtDNA sequence from a representative of each of the infraorders in prosimians has been described until quite recently, and therefore we newly determined complete mtDNA sequences from 5 lemurs, 4 lorises, one tarsier and one platyrrhini. These sequences were provided to phylogenetic analyses in combination with the sequences from the 15 primates species reported to the database. The position of tarsiers among primates could not be resolved by the maximum likelihood (ML) and neighbor-joining (NJ) analyses with several data sets. As to the position of tarsiers, any of the three alternative topologies (monophyly of haplorhini, monophyly of prosimians, and tarsiers being basal in primates) was not rejected at the significance level of 5%, neither at the nucleotide nor at the amino acid level. In addition, the significant variations of C and T compositions were observed across primates species. Furthermore, we used AGY data sets for phylogenetic analyses in order to remove the effect of different C/T composition bias across species. The analyses of AGY data sets provided a medium support for the monophyly of haplorhini, which might have been screened by the variation in base composition of mtDNA across species. To estimates the speciation dates within primates, we analyzed the amino acid sequences of mt-proteins with a Bayesian method of Thorne and Kishino. Divergence dates were estimated as follows for the crown groups: about 35.4 million years ago (mya) for lorisiformes, 55.3 mya for lemuriformes, 64.5 mya for strepsirrhini, 70.1 mya for haplorhini and 76.0 mya for primates. Furthermore, we reexamined the biogeographic scenarios which have been proposed for the origin of strepsirrhini (lemuriformes and lorisiformes) and for the dispersal of the lemuriformes and lorisiformes.

The adaptational strategies of the hindlimb muscles in the Tenrecidae species including the aquatic web-footed tenrec (Limnogale mergulus).

The hindlimb muscles in four species of Tenrecidae (Oryzoryctinae: Talazac long-tailed tenrec and web-footed tenrec, Tenrecinae: lesser hedgehog tenrec, and streaked tenrec), were examined macroscopically. The weight ratios of the muscles to the body in the oryzoryctinid species are larger than those in Tenrecinae, since the Oryzoryctinae species have an obviously smaller body from the evolutionary point of view. It can be primarily pointed out that the adaptation of the body size is different between the two subfamilies, and secondarily, that functional adaptation to locomotion is complete within each subfamily. The weight data and the morphological findings demonstrate that the web-footed tenrec possesses an extraordinary large M. semimembranosus in comparison to the Talazac long-tailed tenrec in their weight ratios. This muscle may act as a strong flexor motor in the knee joint during the aquatic locomotion of the web-footed tenrec. Since the other muscles of the web-footed tenrec are similar to those of the Talazac long-tailed tenrec regards weight ratio data, we think that the web-footed tenrec may have derived from a terrestrial ancestor such as the long-tailed tenrecs. In Tenrecinae the streaked tenrec is equipped with larger Mm. adductores, M. semimembranosus and M. triceps surae than the lesser hedgehog tenrec. This species is adapted to fossorial life derived from non-specialized ancestors within the evolutionary lines of the spiny tenrecs.