Population genetics of mouse lemur vomeronasal receptors: current versus past selection and demographic inference

Abstract Background A major effort is underway to use population genetic approaches to identify loci involved in adaptation. One issue that has so far received limited attention is whether loci that show a phylogenetic signal of positive selection in the past also show evidence of ongoing positive selection at the population level. We address this issue using vomeronasal receptors (VRs), a diverse gene family in mammals involved in intraspecific communication and predator detection. In mouse lemurs, we previously demonstrated that both subfamilies of VRs (V1Rs and V2Rs) show a strong signal of directional selection in interspecific analyses. We predicted that ongoing sexual selection and/or co-evolution with predators may lead to current directional or balancing selection on VRs. Here, we re-sequence 17 VRs and perform a suite of selection and demographic analyses in sympatric populations of two species of mouse lemurs (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. Results M. ravelobensis had consistently higher genetic diversity at VRs than M. murinus. In general, we find little evidence for positive selection, with most loci evolving under purifying selection and one locus even showing evidence of functional loss in M. ravelobensis. However, a few loci in M. ravelobensis show potential evidence of positive selection. Using mismatch distributions and expansion models, we infer a more recent colonisation of the habitat by M. murinus than by M. ravelobensis, which most likely speciated in this region earlier on. Conclusions These findings suggest that the analysis of VR variation is useful in inferring demographic and phylogeographic history of mouse lemurs. In conclusion, this study reveals a substantial heterogeneity over time in selection on VR loci, suggesting that VR evolution is episodic

Population genetics of mouse lemur vomeronasal receptors: current versus past selection and demographic inference.

BACKGROUND: A major effort is underway to use population genetic approaches to identify loci involved in adaptation. One issue that has so far received limited attention is whether loci that show a phylogenetic signal of positive selection in the past also show evidence of ongoing positive selection at the population level. We address this issue using vomeronasal receptors (VRs), a diverse gene family in mammals involved in intraspecific communication and predator detection. In mouse lemurs, we previously demonstrated that both subfamilies of VRs (V1Rs and V2Rs) show a strong signal of directional selection in interspecific analyses. We predicted that ongoing sexual selection and/or co-evolution with predators may lead to current directional or balancing selection on VRs. Here, we re-sequence 17 VRs and perform a suite of selection and demographic analyses in sympatric populations of two species of mouse lemurs (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. RESULTS: M. ravelobensis had consistently higher genetic diversity at VRs than M. murinus. In general, we find little evidence for positive selection, with most loci evolving under purifying selection and one locus even showing evidence of functional loss in M. ravelobensis. However, a few loci in M. ravelobensis show potential evidence of positive selection. Using mismatch distributions and expansion models, we infer a more recent colonisation of the habitat by M. murinus than by M. ravelobensis, which most likely speciated in this region earlier on. CONCLUSIONS: These findings suggest that the analysis of VR variation is useful in inferring demographic and phylogeographic history of mouse lemurs. In conclusion, this study reveals a substantial heterogeneity over time in selection on VR loci, suggesting that VR evolution is episodic

Volatile Urinary Signals of Two Nocturnal Primates, Microcebus murinus and M. lehilahytsara

Mouse lemurs are small, nocturnal, arboreal solitary foragers and are endemic primates of Madagascar. This lifestyle and their high predation risk can explain why mouse lemurs rely heavily on olfaction for intraspecific communication. As they often use urine for this purpose, we investigated dichloromethane extracts of the urine of two mouse lemur species, the gray mouse lemur (Microcebus murinus) and the Godman’s mouse lemur (M. lehilahytsara), using gas-chromatography-mass spectrometry. We detected 977 different volatile compounds of different compound classes in 22 urine extracts obtained from nine M. murinus (four males, five females) and nine M. lehilahytsara (three males, six females) individuals. We compared the volatile profiles of the sexes and species using principal component analyses and discriminant function analyses and detected a significant difference in the urinary profiles of males and females and in the profiles of M. murinus and M. lehilahytsara. These very complex sex- and species-specific signatures could be used for distance communication in the context of species recognition, for mate search and in male-male competition. Our study provides important mechanistic insights into complex chemical signaling pathways in primates that are mirrored, in the case of mouse lemurs, by their extraordinarily rich repertoire of olfactory receptors. The production of highly informative olfactory signals may be complementing the complex acoustic signaling system of these solitary foragers suggesting the existence of a multimodal communication network that should be highly beneficial for any species living in dispersed social networks

Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus)

<p>Abstract</p> <p>Background</p> <p>Pleistocene events have shaped the phylogeography of many taxa worldwide. Their genetic signatures in tropical species have been much less explored than in those living in temperate regions. We analysed the genetic structure of a Malagasy primate species, a mouse lemur with a wide distribution (<it>M. murinus)</it>, in order to investigate such phylogeographic processes on a large tropical island. We also evaluated the effects of anthropogenic pressures (fragmentation/deforestation) and natural features (geographic distance, rivers) on genetic structure in order to complement our understanding of past and present processes of genetic differentiation.</p> <p>Results</p> <p>The analysis of the mitochondrial D-loop sequences of 195 samples from 15 study sites (10 from a continuous forest and five from isolated forest fragments) from two adjacent Inter-River-Systems (IRSs) revealed that forest fragmentation and the river restrict gene flow, thereby leading to an increased genetic differentiation between populations beyond the effect of isolation-by-distance. Demographic simulations detected signals of two successive spatial expansions that could be preliminarily dated to the late Pleistocene and early Holocene. The haplotype network revealed geographic structure and showed deep molecular divergences within and between the IRSs that would be congruent with a two-step colonization scenario.</p> <p>Conclusions</p> <p>This study supports the hypothesis of a relatively recent spatial expansion of the grey mouse lemur in northwestern Madagascar, which may also explain why this taxon, in contrast to its congeners, has not yet undergone allopatric speciation in the studied area and possibly across its presently wide range.</p

Long-term host–pathogen evolution of endogenous beta- and gammaretroviruses in mouse lemurs with little evidence of recent retroviral introgression

Madagascar’s flora and fauna have evolved in relative isolation since the island split from the African and Indian continents. When the last common ancestors of lemurs left Africa between 40 and 70 million years ago, they carried a subset of the viral diversity of the mainland population within them, which continued to evolve throughout the lemur radiation. Relative to other primate radiations, we know very little about the past or present viral diversity of lemurs, particularly mouse lemurs. Using high-throughput sequencing, we identified two gammaretroviruses and three betaretroviruses in the genomes of four species of wild mouse lemurs. The two gammaretroviruses and two betaretroviruses have not previously been described. One betaretrovirus was previously identified. All identified viruses are present in both Lorisiformes and Lemuriformes but absent from haplorrhine primates. The estimated ages of these viruses are consistent with the estimated divergence dates of the host lineages, suggesting they colonized the lemur genome after the Haplorrhine–Strepsirrhine split, but before the Lorisiformes–Lemuriformes split and before the colonization of Madagascar. The viral phylogenies connect multiple lineages of retroviruses from non-lemur and non-Madagascar-native species, suggesting substantial cross-species transmission occurred deep in the primate clade prior to its geographic dispersal. These phylogenies provide novel insights into known retroviral clades. They suggest that the origin of gammaretroviruses in rodents or bats may be premature and that the Jaagsiekte sheep virus clade may be older and more broadly distributed among mammals than previously thought

Abundance and conservation status of two newly described lemur species in northwestern Madagascar (Microcebus danfossi, Lepilemur grewcockorum)

The distribution and abundance of Danfoss’ mouse lemurs (Microcebus danfossi) and Grewcock’s sportive lemurs (Lepilemur grewcockorum), two regional endemics from northwestern Madagascar, were studied from May to December 2008 in the Sofia region between the rivers Sofia and Maevarano. The goal was to investigate the size and quality of forest fragments and to determine the presence and abundance of the recently described M. danfossi and L. grewcockorum. They are confined to this region and their conservation status has not yet been determined. A total of eleven sites were visited and systematic census observations were carried out in each of them. M. danfossi was present in ten of eleven sites and its abundance ranged from 4.5 to 8.5 individuals per kilometer. L. grewcockorum was present in only three of eleven sites and its abundance ranged from 0.8 to one individual per kilometre. Based on the results of this study M. danfossi should be listed as Vulnerable and L. grewcockorum as Endangered. Based on the abundance data, the size and the general condition of the fragments, the forests of Anjajavy, Ambarijeby and Bekofafa are most favorable for future protection, because they still contain the most intact nocturnal lemur communities.RÉSUMÉUne étude sur la distribution et l’abondance de Microcebus danfossi et Lepilemur grewcockorum, deux espèces endémiques de la région Nord - ouest de Madagascar, a été effectuée dans la région de Sofia, entre les fleuves Sofia et Maevarano, de mai à décembre 2008. Les objectifs étaient d’évaluer la qualité et la largeur des fragments forestiers restants ainsi que de déterminer la diversité de lémuriens nocturnes dans la région. Nous avons aussi prévu de détecter des sites potentiels en vue de la conservation de fragments présentant une biodiversité riche, en particulier en ce qui concerne les espèces de lémuriens nocturnes récemment décrites dans cette région, M. danfossi et L. grewcockorum. Enfin, nous avons récolté toutes les informations disponibles afin de proposer une classification objective pour chaque espèce conformément aux critères de l’IUCN. Nous avons inventorié onze sites au total, à savoir la forêt d’Anjajavy, le savoka du village d’Antonibe, la forêt d’Antambato, le savoka d’Antsatrana, la forêt de Beanamalao, la forêt de Betsatsika, la forêt d’Ambarijeby, la forêt d’Ankaramikely, la forêt de Bekofafa, les savoka d’Ambararata et de Mahadera. Dans chaque site de ces sites, nous avons évalué la qualité de la forêt (signe de feu, déboisement, trouées) et la surface du fragment avant de réaliser six inventaires nocturnes le long de deux pistes de 1 km de longueur. Nous avons identifié de deux à quatre espèces de lémuriens nocturnes par site et au total cinq espèces ont été recensées. M. danfossi était présent dans dix sites et son abondance variait de 4,5 à 8,5 individus par kilomètre. L. grewcockorum n’était présent que dans trois sites et son abondance variait de 0,8 à 1,0 individu par kilomètre. Les fragments avaient des superficies comprises entre 50 et 400 ha. Les forêts d’Anjajavy, d’Ankaramikely, d’Antambato et de Bekofafa se sont avérées être les meilleurs sites en matière de qualité de la forêt. Compte tenu du degré de fragmentation, des pressions anthropiques et de nos résultats d’inventaire de ces deux espèces endémiques, nous proposons un statut de conservation Vulnérable pour M. danfossi et En Danger pour L. grewcockorum. Nous proposons également de considérer la protection des forêts d’Anjajavy, d’Ambarijeby et de Bekofafa dans la mesure où elles sont encore intactes et abritent un assez grand nombre d’espèces de lémuriens

Dispersal and genetic structures in a tropical small mammal, the Bornean tree shrew (Tupaia longipes), in a fragmented landscape along the Kinabatangan River, Sabah, Malaysia

Background Constraints in migratory capabilities, such as the disruption of gene flow and genetic connectivity caused by habitat fragmentation, are known to affect genetic diversity and the long-term persistence of populations. Although negative population trends due to ongoing forest loss are widespread, the consequence of habitat fragmentation on genetic diversity, gene flow and genetic structure has rarely been investigated in Bornean small mammals. To fill this gap in knowledge, we used nuclear and mitochondrial DNA markers to assess genetic diversity, gene flow and the genetic structure in the Bornean tree shrew, Tupaia longipes, that inhabits forest fragments of the Lower Kinabatangan Wildlife Sanctuary, Sabah. Furthermore, we used these markers to assess dispersal regimes in male and female T. longipes. Results In addition to the Kinabatangan River, a known barrier for dispersal in tree shrews, the heterogeneous landscape along the riverbanks affected the genetic structure in this species. Specifically, while in larger connected forest fragments along the northern riverbank genetic connectivity was relatively undisturbed, patterns of genetic differentiation and the distribution of mitochondrial haplotypes in a local scale indicated reduced migration on the strongly fragmented southern riverside. Especially, oil palm plantations seem to negatively affect dispersal in T. longipes. Clear sex-biased dispersal was not detected based on relatedness, assignment tests, and haplotype diversity. Conclusion This study revealed the importance of landscape connectivity to maintain migration and gene flow between fragmented populations, and to ensure the long-term persistence of species in anthropogenically disturbed landscapes

Messing about on the river: the role of geographic barriers in shaping the genetic structure of Bornean small mammals in a fragmented landscape

Landscape features may restricting dispersal and gene flow, and increase demographic isolation among sub-populations. In addition, landscape features may represent potential dispersal barriers depending on species vagility. To predict the persistence of populations and to formulate adequate conservation measures it is essential to understand the ability of species to transverse landscape barriers. Using population genetic techniques we assessed the importance of physical barriers along the Kinabatangan River for a suite of non-volant small mammals. Cytochrome b sequence variation was examined for each of the 19 species sampled across both riverbanks. Haplotype networks and molecular variance analyses indicated contrasting patterns of genetic isolation between riversides for different taxa. Genetic isolation between riversides ranged from moderate to complete in tree shrews and squirrels, whereas no isolating effect could be detected in murids and gymnures. Although genetic divergence between forest fragments on the same side of the river could only be studied in a subset of six species, the results suggest an additional dispersal barrier for two of these studied species. While barrier effects of a paved road and tributaries could not be verified, large oil palm plantations seem to have disrupted gene flow in these species. Furthermore, the findings suggest higher genetic connectivity on the more continuously forested compared to the more fragmented riverside, and underline the importance of forest corridors as essential conservation measures to maintain genetic diversity in a fragmented landscape such as that along the Kinabatangan River