True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex

Neuropeptide receptor distributions in male and female Eulemur vary between female-dominant and egalitarian species

Aggression and its neurochemical modulators are typically studied in males, leaving the mechanisms of female competitive aggression or dominance largely unexplored. To better understand how competitive aggression is regulated in the primate brain, we used receptor autoradiography to compare the neural distributions of oxytocin and vasopressin receptors in male and female members of female-dominant versus egalitarian/codominant species within the Eulemur genus, wherein dominance structure is a reliable proxy of aggression in both sexes. We found that oxytocin receptor binding in the central amygdala (CeA) was predicted by dominance structure, with the members of three codominant species showing more oxytocin receptor binding in this region than their peers in four female-dominant species. Thus, both sexes in female-dominant Eulemur show a pattern consistent with the regulation of aggression in male rodents. We suggest that derived pacifism in Eulemur stems from selective suppression of ancestral female aggression over evolutionary time via a mechanism of increased oxytocin receptor binding in the CeA, rather than from augmented male aggression. This interpretation implies fitness costs to female aggression and/or benefits to its inhibition. These data establish Eulemur as a robust model for examining neural correlates of male and female competitive aggression, potentially providing novel insights into female dominance.

A Pervasive History of Gene Flow in Madagascar's True Lemurs (Genus Eulemur)

In recent years, it has become widely accepted that interspecific gene flow is common across the Tree of Life. Questions remain about how species boundaries can be maintained in the face of high levels of gene flow and how phylogeneticists should account for reticulation in their analyses. The true lemurs of Madagascar (genus Eulemur, 12 species) provide a unique opportunity to explore these questions, as they form a recent radiation with at least five active hybrid zones. Here, we present new analyses of a mitochondrial dataset with hundreds of individuals in the genus Eulemur, as well as a nuclear dataset containing hundreds of genetic loci for a small number of individuals. Traditional coalescent-based phylogenetic analyses of both datasets reveal that not all recognized species are monophyletic. Using network-based approaches, we also find that a species tree containing between one and three ancient reticulations is supported by strong evidence. Together, these results suggest that hybridization has been a prominent feature of the genus Eulemur in both the past and present. We also recommend that greater taxonomic attention should be paid to this group so that geographic boundaries and conservation priorities can be better established.

Toward Passive Acoustic Monitoring of Lemurs: Using an Affordable Open-Source System to Monitor Phaner Vocal Activity and Density

Developing new cost-effective methods for monitoring the distribution and abundance of species is essential for conservation biology. Passive acoustic monitoring (PAM) has long been used in marine mammals and has recently been postulated to be a promising method to improve monitoring of terrestrial wildlife as well. Because Madagascar’s lemurs are among the globally most threatened taxa, this study was designed to assess the applicability of an affordable and open-source PAM device to estimate the density of pale fork-marked lemurs (Phaner pallescens). Using 12 playback experiments and one fixed transect of four automated acoustic recorders during one night of the dry season in Kirindy Forest, we experimentally estimated the detection space for Phaner and other lemur vocalizations. Furthermore, we manually annotated more than 10,000 vocalizations of Phaner from a single location and used bout rates from previous studies to estimate density within the detection space. To truncate detections beyond 150 m, we applied a sound pressure level (SPL) threshold filtering out vocalizations below SPL 50 (dB re 20 μPa). During the dry season, vocalizations of Phaner can be detected with confidence beyond 150 m by a human listener. Within our fixed truncated detection area corresponding to an area of 0.07 km2 (detection radius of 150 m), we estimated 10.5 bouts per hour corresponding to a density of Phaner of 38.6 individuals/km2. Our density estimates are in line with previous estimates based on individually marked animals conducted in the same area. Our findings suggest that PAM also could be combined with distance sampling methods to estimate densities. We conclude that PAM is a promising method to improve the monitoring and conservation of Phaner and many other vocally active primates.

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs

Gastrointestinal helminth-microbiota associations are shaped by various ecological processes. The effect of the ecological context of the host on the bacterial microbiome and gastrointestinal helminth parasites has been tested in a number of ecosystems and experimentally. This study takes the important step to look at these two groups at the same time and to start to examine how these communities interact in a changing host environment. Fresh faecal samples (N = 335) from eight wild Eulemur populations were collected over 2 years across Madagascar. We used 16S ribosomal RNA gene sequencing to characterise the bacterial microbiota composition, and faecal flotation to isolate and morphologically identify nematode eggs. Infections with nematodes of the genera Callistoura and Lemuricola occurred in all lemur populations. Seasonality significantly contributed to the observed variation in microbiota composition, especially in the dry deciduous forest. Microbial richness and Lemuricola spp. infection prevalence were highest in a previously intensely logged site, whereas Callistoura spp. showed no such pattern. In addition, we observed significant correlations between gastrointestinal parasites and bacterial microbiota composition in these lemurs, with 0.4-0.7% of the variation in faecal bacterial microbiota composition being explained by helminth infections. With this study, we show effects of environmental conditions on gastrointestinal nematodes and bacterial interactions in wild lemurs and believe it is essential to consider the potential role of microbiome-parasite associations on the hosts' GI stability, health, and survival.

Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species

A significant number of Southeast Asian mammal species described in the 19^th and 20^th century were subsequently synonymized and are now considered subspecies. Many are affected by rapid habitat loss which creates an urgent need to re-assess the conservation status based on species boundaries established with molecular data. However, such data are lacking and difficult to obtain for many populations and subspecies. We document via a literature survey and empirical study how shotgun sequencing of faecal DNA is a still underutilized but powerful tool for accelerating such evaluations. We obtain 11 mitochondrial genomes for three subspecies in the langur genus Presbytis through shotgun sequencing of faecal DNA (P. femoralis femoralis, P. f. percura, P. siamensis cf. cana). The genomes support the resurrection of all three subspecies to species based on multiple species delimitation algorithms (PTP, ABGD, Objective Clustering) applied to a dataset covering 40 species and 43 subspecies of Asian colobines. For two of the newly recognized species (P. femoralis, P. percura), the results lead to an immediate change in IUCN status to Critically Endangered due to small population sizes and fragmented habitats. We conclude that faecal DNA should be more widely used for clarifying species boundaries in endangered mammals.

Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods

The major histocompatibility complex (MHC) is a highly polymorphic and polygenic genomic region that plays a crucial role in immune-related diseases. Given the need for comparative studies on the variability of immunologically important genes among wild populations and species, we investigated the allelic variation of MHC class II DRB among three congeneric true lemur species: the red-fronted lemur (Eulemur rufifrons), red-bellied lemur (Eulemur rubriventer), and black lemur (Eulemur macaco). We noninvasively collected hair and faecal samples from these species across different regions in Madagascar. We assessed DRB exon 2 polymorphism with a newly developed primer set, amplifying nearly all non-synonymous codons of the antigen-binding sites. We defined 26 DRB alleles from 45 individuals (17 alleles from E. rufifrons (N = 18); 5 from E. rubriventer (N = 7); and 4 from E. macaco (N = 20). All detected alleles are novel and show high levels of nucleotide (26.8%) and non-synonymous codon polymorphism (39.4%). In these lemur species, we found neither evidence of a duplication of DRB genes nor a sharing of alleles among sympatric groups or allopatric populations of the same species. The non-sharing of alleles may be the result of a geographical separation over a long time span and/or different pathogen selection pressures. We found dN/dS rates > 1 in the functionally important antigen recognition sites, providing evidence for balancing selection. Especially for small and isolated populations, quantifying and monitoring DRB variation are recommended to establish successful conservation plans that mitigate the possible loss of immunogenetic diversity in lemurs.

The role of facial pattern variation for species recognition in red-fronted lemurs (Eulemur rufifrons)

BACKGROUND

Species recognition, i.e., the ability to distinguish conspecifics from heterospecifics, plays an essential role in reproduction. The role of facial cues for species recognition has been investigated in several non-human primate species except for lemurs. We therefore investigated the role of facial cues for species recognition in wild red-fronted lemurs (Eulemur rufifrons) at Kirindy Forest. We presented adult red-fronted lemurs pictures of male faces from five species including red-fronted lemurs, three closely related species, white-fronted lemurs (E. albifrons), brown lemurs (E. fulvus), rufous brown lemurs (E. rufus), and genetically more distant red-bellied lemurs (E. rubriventer), occurring in allopatry with the study population. We predicted that red-fronted lemurs respond stronger to conspecific than to heterospecific pictures and that females show stronger responses than males. In addition, if genetic drift has played a role in the evolution of facial color patterns in the members of this genus, we predicted that responses of red-fronted lemurs correlate negatively with the genetic distance to the different species stimuli.

RESULTS

Red-fronted lemurs looked significantly longer at pictures of their own species than at those of heterospecifics. Females spent less time looking at pictures of white-fronted, brown and red-bellied lemurs than males did, but not to pictures of red-bellied lemurs and a control stimulus. Individuals also exhibited sniffing behavior while looking at visual stimuli, and the time spent sniffing was significantly longer for pictures of conspecifics compared to those of heterospecifics. Moreover, the time spent looking and sniffing towards the pictures correlated negatively with the genetic distance between their own species and the species presented as stimulus.

CONCLUSIONS

We conclude that red-fronted lemurs have the ability for species recognition using visual facial cues, which may allow them to avoid costly interbreeding. If so, sexual selection might have influenced the evolution of facial patterns in eulemurs. Since responses also correlated with genetic distance, our findings suggest a potential role of genetic drift as well as sexual selection in influencing the evolution of facial variation in eulemurs. Because study subjects looked and sniffed towards the presented pictures, red-fronted lemurs might have the ability for multi-modal species recognition.

Testing the adaptive radiation hypothesis for the lemurs of Madagascar

Lemurs, the diverse, endemic primates of Madagascar, are thought to represent a classic example of adaptive radiation. Based on the most complete phylogeny of living and extinct lemurs yet assembled, I tested predictions of adaptive radiation theory by estimating rates of speciation, extinction and adaptive phenotypic evolution. As predicted, lemur speciation rate exceeded that of their sister clade by nearly twofold, indicating the diversification dynamics of lemurs and mainland relatives may have been decoupled. Lemur diversification rates did not decline over time, however, as predicted by adaptive radiation theory. Optimal body masses diverged among dietary and activity pattern niches as lineages diversified into unique multidimensional ecospace. Based on these results, lemurs only partially fulfil the predictions of adaptive radiation theory, with phenotypic evolution corresponding to an 'early burst' of adaptive differentiation. The results must be interpreted with caution, however, because over the long evolutionary history of lemurs (approx. 50 million years), the 'early burst' signal of adaptive radiation may have been eroded by extinction.

The role of acoustic signals for species recognition in redfronted lemurs (Eulemur rufifrons)

BACKGROUND

Signals are essential for communication and play a fundamental role in the evolution and diversification of species. Olfactory, visual and acoustic species-specific signals have been shown to function for species recognition in non-human primates, but the relative contributions of selection for species recognition driven by sexual selection, natural selection, or genetic drift for the diversification of these signals remain largely unexplored. This study investigates the importance of acoustic signals for species recognition in redfronted lemurs (Eulemur rufifrons). We conducted playback experiments in both major populations of this species separated by several hundred kilometers: Kirindy Forest in the west and Ranomafana National Park in the east of Madagascar. The playback stimuli were composed of species-specific loud calls of E. rufifrons, three closely related species (E. albifrons, E. fulvus and E. rufus) and one genetically more distant species (E. rubriventer) that occurs in sympatry with eastern redfronted lemurs. We tested the ability of redfronted lemurs to discriminate conspecific from heterospecific loud calls by measuring the time spent looking towards the speaker after presentation of each loud call. We also tested the difference between female and male responses because loud calls may play a role in mate choice and the avoidance of heterospecific mating.

RESULTS

Redfronted lemurs in Kirindy Forest did not discriminate their own loud calls from those of E. albifrons, E. fulvus and E. rufus, but they discriminated loud calls of E. rubriventer from their own. The Ranomafana population was tested only with three playback stimuli (E. rufifrons, E. albifrons, E. rubriventer) and did not discriminate between their own loud calls and those of E. albifrons and E. rubriventer. The response of females and males to playbacks did not differ in both populations. However, subjects in Ranomafana National Park responded more strongly to playback stimuli from E. rubriventer than subjects in Kirindy Forest.

CONCLUSIONS

We conclude that in both populations individuals were not able to discriminate between loud calls of closely related species living in allopatry and that responses to more distantly related congeners are likely to be modulated by experience. Subjects in Ranomafana paid more attention to loud calls of syntopic E. rubriventer in comparison to the Kirindy subjects, suggesting that experience is important in facilitating discrimination. Because acoustic and genetic distances among eulemurs are correlated, diversification in their acoustic signals might be the result of genetic drift.

Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae)

BACKGROUND

The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes.

RESULTS

Intraspecific molecular and morphological differentiation is visible among many populations. Genomes of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, π and θ). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs.

CONCLUSIONS

We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (with L. bocagei in the Tejo, with L. microcephalus and L. sclateri in the Guadiana). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.

The use of museum specimens with high-throughput DNA sequencers

Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.

Defining species in an advanced technological landscape

The answer to the proffered question, "What is a species?" is considered one of the fundamental issues of biological science, as well as one of the most polarizing and sometimes acrimonious problems. Dozens of species concepts have been defined, but none are universal for implementation across all taxa. Within the past thirty years, the ability to analyze DNA data has progressed to the point that multiple methodologies can be simultaneously applied to the same evolutionary questions. The use of restriction fragment length polymorphisms, microsatellites, and mitochondrial (mtDNA) and nuclear DNA (nucDNA) sequence data has unarguably changed how we look at diversity and intensified the concept debate through the proliferation of species descriptions. Over the past two decades, Madagascar's biodiversity has gone through a tremendous taxonomic expansion by the elevation of subspecies to species and through novel descriptions, especially within the nocturnal lemurs. With the tremendous continuous loss of habitat, exponential human population growth, and stochastic changes predicted over coming decades, elucidating the earth's biodiversity will never be more important than now. Here, we examine species concepts and their attendant criteria. We predict how technological advances will alter, improve and, we hope, fully consolidate the unity of thoughts related to this central topic of evolutionary biology and its numerous interconnected disciplines.

Phylogeographic analysis of the true lemurs (genus Eulemur) underlines the role of river catchments for the evolution of micro-endemism in Madagascar

INTRODUCTION

Due to its remarkable species diversity and micro-endemism, Madagascar has recently been suggested to serve as a biogeographic model region. However, hypothesis-based tests of various diversification mechanisms that have been proposed for the evolution of the island's micro-endemic lineages are still limited. Here, we test the fit of several diversification hypotheses with new data on the broadly distributed genus Eulemur using coalescent-based phylogeographic analyses.

RESULTS

Time-calibrated species tree analyses and population genetic clustering resolved the previously polytomic species relationships among eulemurs. The most recent common ancestor of eulemurs was estimated to have lived about 4.45 million years ago (mya). Divergence date estimates furthermore suggested a very recent diversification among the members of the "brown lemur complex", i.e. former subspecies of E. fulvus, during the Pleistocene (0.33-1.43 mya). Phylogeographic model comparisons of past migration rates showed significant levels of gene flow between lineages of neighboring river catchments as well as between eastern and western populations of the redfronted lemur (E. rufifrons).

CONCLUSIONS

Together, our results are concordant with the centers of endemism hypothesis (Wilmé et al. 2006, Science 312:1063-1065), highlight the importance of river catchments for the evolution of Madagascar's micro-endemic biota, and they underline the usefulness of testing diversification mechanisms using coalescent-based phylogeographic methods.