"Life history space": a multivariate analysis of life history variation in extant and extinct Malagasy lemurs

Evidence for female dominance in the Milne-Edwards' sportive lemur (Lepilemur edwardsi)

Female dominance over males is more frequent in Malagasy lemurs than in other primate clades, but patterns of female-male dominance vary among species, and few data are available for one particularly species-rich genus, Lepilemur. We investigated the types, temporal distribution, and outcome of female-male agonistic conflicts in the Milne-Edwards' sportive lemur (Lepilemur edwardsi). Ten L. edwardsi belonging to five social units were equipped with radio collars and observed during 79 focal follows between May and November 1998. We quantified agonistic conflicts, monthly conflict rates, and documented the winner and context for all conflicts. Female-male agonistic conflicts (N = 162) occurred at a mean rate of 0.21 conflicts/hour within groups. Agonistic conflicts peaked during the birth season and occurred mostly in unknown or infant proximity contexts. Females won 96% of all decided agonistic conflicts (N = 154). Other outcomes occurred only when females were with infants during the birth season. In that context, one female sometimes withdrew from her pair partner, and another female withdrew or fled from an extra-group male whose attacks eventually led to infanticide. Our results suggest female dominance in pair-living L. edwardsi. We hypothesize that elevated female aggression may convey fitness benefits to female Lepilemur because it generally allows females to intervene quickly and efficiently on behalf of their infants against nonfather males who may approach the newborn infants when they are parked in vegetation.

Mammalian Life History: Weaning and Tooth Emergence in a Seasonal World

The young of toothed mammals must have teeth to reach feeding independence. How tooth eruption integrates with gestation, birth and weaning is examined in a life-history perspective for 71 species of placental mammals. Questions developed from high-quality primate data are then addressed in the total sample. Rather than correlation, comparisons focus on equivalence, sequence, the relation to absolutes (six months, one year), the distribution of error and adaptive extremes. These mammals differ widely at birth, from no teeth to all deciduous teeth emerging, but commonalities appear when infants transit to independent feeding. Weaning follows completion of the deciduous dentition, closest in time to emergence of the first permanent molars and well before second molars emerge. Another layer of meaning appears when developmental age is counted from conception because the total time to produce young feeding independently comes up against seasonal boundaries that are costly to cross for reproductive fitness. Mammals of a vast range of sizes and taxa, from squirrel monkey to moose, hold conception-to-first molars in just under one year. Integrating tooth emergence into life history gives insight into living mammals and builds a framework for interpreting the fossil record.

The Island of Female Power? Intersexual Dominance Relationships in the Lemurs of Madagascar

The extant primates of Madagascar (Lemuriformes) represent the endpoints of an adaptive radiation following a single colonization event more than 50 million years ago. They have since evolved a diversity of life history traits, ecological adaptations and social systems that rivals that of all other living primates combined. Their social systems are characterized by a unique combination of traits, including the ability of adult females to dominate adult males. In fact, there is no other group of mammals in which female dominance is so widespread. Yet, recent research has indicated that there is more interspecific variation in lemur intersexual relationships than previously acknowledged. Here, we therefore review and summarize the relevant literature, quantifying the extent of sex-bias in intersexual dominance relations documented in observational and experimental studies in captivity and the wild. Female dominance is often, but not always, implemented by spontaneous male submission in the absence of female aggression and linked to female sexual maturation. We connect the available evidence to the hypotheses that have been proposed to explain the evolution of female dominance among lemurs. The occurrence of female dominance in all lemur families and the interspecific variation in its extent indicate that it has evolved soon after lemurs colonized Madagascar – presumably in response to particular ecological challenges – and that it has since been reduced in magnitude independently in some taxa. Our study contributes important comparative information on sex roles from an independent primate radiation and provides general insights into the conditions, opportunities and obstacles in the evolution of female-biased power.

Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

A new interpretation of Madagascar's megafaunal decline: The "Subsistence Shift Hypothesis"

Fundamental disagreements remain regarding the relative importance of climate change and human activities as triggers for Madagascar's Holocene megafaunal extinction. We use stable isotope data from stalagmites from northwest Madagascar coupled with radiocarbon and butchery records from subfossil bones across the island to investigate relationships between megafaunal decline, climate change, and habitat modification. Archaeological and genetic evidence support human presence by 2000 years Before Common Era (BCE). Megafaunal decline was at first slow; it hastened at ∼700 Common Era (CE) and peaked between 750 and 850 CE, just before a dramatic vegetation transformation in the northwest that resulted in the replacement of C₃ woodland habitat with C₄ grasslands, during a period of heightened monsoonal activity. Cut and chop marks on subfossil lemur bones reveal a shift in primary hunting targets from larger, now-extinct species prior to ∼900 CE, to smaller, still-extant species afterwards. By 1050 CE, megafaunal populations had essentially collapsed. Neither the rapid megafaunal decline beginning ∼700 CE, nor the dramatic vegetation transformation in the northwest beginning ∼890 CE, was influenced by aridification. However, both roughly coincide with a major transition in human subsistence on the island from hunting/foraging to herding/farming. We offer a new hypothesis, which we call the "Subsistence Shift Hypothesis," to explain megafaunal decline and extinction in Madagascar. This hypothesis acknowledges the importance of wild-animal hunting by early hunter/foragers, but more critically highlights negative impacts of the shift from hunting/foraging to herding/farming, settlement by new immigrant groups, and the concomitant expansion of the island's human population. The interval between 700 and 900 CE, when the pace of megafaunal decline quickened and peaked, coincided with this economic transition. While early megafaunal decline through hunting may have helped to trigger the transition, there is strong evidence that the economic shift itself hastened the crash of megafaunal populations.

Population viability and harvest sustainability for Madagascar lemurs

Subsistence hunting presents a conservation challenge by which biodiversity preservation must be balanced with safeguarding of human livelihoods. Globally, subsistence hunting threatens primate populations, including Madagascar's endemic lemurs. We used population viability analysis to assess the sustainability of lemur hunting in Makira Natural Park, Madagascar. We identified trends in seasonal hunting of 11 Makira lemur species from household interview data, estimated local lemur densities in populations adjacent to focal villages via transect surveys, and quantified extinction vulnerability for these populations based on species-specific demographic parameters and empirically derived hunting rates. We compared stage-based Lefkovitch with periodic Leslie matrices to evaluate the impact of regional dispersal on persistence trajectories and explored the consequences of perturbations to the timing of peak hunting relative to the lemur birth pulse, under assumptions of density-dependent reproductive compensation. Lemur hunting peaked during the fruit-abundant wet season (March-June). Estimated local lemur densities were roughly inverse to body size across our study area. Life-history modeling indicated that hunting most severely threatened the species with the largest bodies (i.e., Hapalemur occidentalis, Avahi laniger, Daubentonia madagascariensis, and Indri indi), characterized by late-age reproductive onsets and long interbirth intervals. In model simulations, lemur dispersal within a regional metapopulation buffered extinction threats when a majority of local sites supported growth rates above the replacement level but drove regional extirpations when most local sites were overharvested. Hunt simulations were most detrimental when timed to overlap lemur births (a reality for D. madagascariensis and I. indri). In sum, Makira lemurs were overharvested. Regional extirpations, which may contribute to broad-scale extinctions, will be likely if current hunting rates persist. Cessation of anthropogenic lemur harvest is a conservation priority, and development programs are needed to help communities switch from wildlife consumption to domestic protein alternatives.

Dental development and age at death of the holotype of Anapithecus hernyaki (RUD 9) using synchrotron virtual histology

The chronology of dental development and life history of primitive catarrhines provides a crucial comparative framework for understanding the evolution of hominoids and Old World monkeys. Among the extinct groups of catarrhines are the pliopithecoids, with no known descendants. Anapithecus hernyaki is a medium-size stem catarrhine known from Austria, Hungary and Germany around 10 Ma, and represents a terminal lineage of a clade predating the divergence of hominoids and cercopithecoids, probably more than 30 Ma. In a previous study, Anapithecus was characterized as having fast dental development. Here, we used non-destructive propagation phase contrast synchrotron micro-tomography to image several dental microstructural features in the mixed mandibular dentition of RUD 9, the holotype of A. hernyaki. We estimate its age at death to be 1.9 years and describe the pattern, sequence and timing of tooth mineralization. Our results do not support any simplistic correlation between body mass and striae periodicity, since RUD 9 has a 3-day periodicity, which was previously thought unlikely based on body mass estimates in Anapithecus. We demonstrate that the teeth in RUD 9 grew even faster and initiated even earlier in development than suggested previously. Permanent first molars and the canine initiated 49 and 38 days prenatally, respectively. These results contribute to a better understanding of dental development in Anapithecus and may provide a window into the dental development of the last common ancestor of hominoids and cercopithecoids.

Lemur Biorhythms and Life History Evolution

Skeletal histology supports the hypothesis that primate life histories are regulated by a neuroendocrine rhythm, the Havers-Halberg Oscillation (HHO). Interestingly, subfossil lemurs are outliers in HHO scaling relationships that have been discovered for haplorhine primates and other mammals. We present new data to determine whether these species represent the general lemur or strepsirrhine condition and to inform models about neuroendocrine-mediated life history evolution. We gathered the largest sample to date of HHO data from histological sections of primate teeth (including the subfossil lemurs) to assess the relationship of these chronobiological measures with life history-related variables including body mass, brain size, age at first female reproduction, and activity level. For anthropoids, these variables show strong correlations with HHO conforming to predictions, though body mass and endocranial volume are strongly correlated with HHO periodicity in this group. However, lemurs (possibly excepting Daubentonia) do not follow this pattern and show markedly less variability in HHO periodicity and lower correlation coefficients and slopes. Moreover, body mass is uncorrelated, and brain size and activity levels are more strongly correlated with HHO periodicity in these animals. We argue that lemurs evolved this pattern due to selection for risk-averse life histories driven by the unpredictability of the environment in Madagascar. These results reinforce the idea that HHO influences life history evolution differently in response to specific ecological selection regimes.

Larger mammalian body size leads to lower retroviral activity

Retroviruses have been infecting mammals for at least 100 million years, leaving descendants in host genomes known as endogenous retroviruses (ERVs). The abundance of ERVs is partly determined by their mode of replication, but it has also been suggested that host life history traits could enhance or suppress their activity. We show that larger bodied species have lower levels of ERV activity by reconstructing the rate of ERV integration across 38 mammalian species. Body size explains 37% of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding due to other life history traits. Furthermore, 68% of the variance in the mean age of ERVs per genome can also be explained by body size. These results indicate that body size limits the number of recently replicating ERVs due to their detrimental effects on their host. To comprehend the possible mechanistic links between body size and ERV integration we built a mathematical model, which shows that ERV abundance is favored by lower body size and higher horizontal transmission rates. We argue that because retroviral integration is tumorigenic, the negative correlation between body size and ERV numbers results from the necessity to reduce the risk of cancer, under the assumption that this risk scales positively with body size. Our model also fits the empirical observation that the lifetime risk of cancer is relatively invariant among mammals regardless of their body size, known as Peto's paradox, and indicates that larger bodied mammals may have evolved mechanisms to limit ERV activity.

Retroviruses have been invading mammalian genomes for over 100 million years, leaving traces known as endogenous retroviruses (ERVs). Early genome sequencing studies revealed a marked difference in the activity of retroviruses among species, with humans largely containing inactive lineages of ERVs, while the mouse contains numerous lineages of active ERVs. We explore the hypothesis that life history traits determine the activity of ERVs in mammalian genomes, and show that larger mammals have fewer ERV copies over recent evolutionary time (the last 10 million years) compared to smaller mammals. This association is determined by body size independently of any confounding variables. We build a mathematical model that shows that ERV abundance in genomes decreases with larger body size and increases with horizontal transmission. Retroviral integration can cause cancer, and our analysis suggests that larger bodied animals control ERV replication in order to postpone cancer until a post-reproductive age. This is in line with a long-standing observation that cancer rates do not fluctuate among mammals of different body size, a phenomenon known as Peto's paradox, and opens up the possibility that larger animals have evolved mechanisms to limit ERV activity.

Dietary reconstruction of Pliocene Parapapio whitei from Makapansgat, South Africa, using dental microwear texture analysis

Pliocene Parapapio whitei fossils from Makapansgat have yielded stable isotope values suggesting some foraging on C4 plants and possibly underground storage organs (USOs). Dental microwear texture analysis on Pp.whitei (M 3147, MP 62, MP 223 and MP 239) from Makapansgat Members 3-4 is performed to examine whether tooth surface damage from mastication agrees with prior dietary inferences from isotopes. The enamel surface texture of Pp. whitei is relatively complex, resembling Lophocebus albigena and Cebusapella, and lacks the anisotropy of Trachypithecuscristatus and Alouattapalliata. The textural fill volume of Pp. whitei is distinct from extant forest primates suggesting extremes in hard-object consumption. Grit adhering to USOs is offered as an explanation for these enamel textural properties, corroborating the inference that Pp. whitei supplemented its diet with terrestrial resources. © 2013 S. Karger AG, Basel.

Beware of primate life history data: a plea for data standards and a repository

Life history variables such as the age at first reproduction and the interval between consecutive births are measures of investment in growth and reproduction in a particular population or species. As such they allow for meaningful comparisons of the speed of growth and reproduction between species and between larger taxa. Especially in primates such life history research has far reaching implications and has led for instance to the "grandmother hypothesis". Other links have been proposed with respect to dietary adaptations: Because protein is essential for growth and one of the primary sources of protein, leaves, occurs much less seasonally than fruits, it has been predicted that folivorous primates should grow faster compared to frugivorous ones. However, when comparing folivorous Asian colobines with frugivorous Asian macaques we recently documented a longer, instead of a shorter gestation length in folivores while age at first reproduction and interbirth interval did not differ. This supports earlier findings for Malagasy lemurs in which all life history variables tested were significantly longer in folivores compared to frugivores. Wondering why these trends were not apparent sooner, we tried to reconstruct our results for Asian primates with data from four popular life history compilations. However, this attempt failed; even the basic, allometric relationship with adult female body mass that is typical for life history variables could not be recovered. This negative result hints at severe problems with data quality. Here we show that data quality can be improved significantly by standardizing the variables and by controlling for factors such as nutritional conditions or infant mortality. Ideally, in the future, revised primate life history data should be collated in a central database accessible to everybody. In the long run such an initiative should be expanded to include all mammalian species.

Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar

We performed a population genomics study of the aye-aye, a highly specialized nocturnal lemur from Madagascar. Aye-ayes have low population densities and extensive range requirements that could make this flagship species particularly susceptible to extinction. Therefore, knowledge of genetic diversity and differentiation among aye-aye populations is critical for conservation planning. Such information may also advance our general understanding of Malagasy biogeography, as aye-ayes have the largest species distribution of any lemur. We generated and analyzed whole-genome sequence data for 12 aye-ayes from three regions of Madagascar (North, West, and East). We found that the North population is genetically distinct, with strong differentiation from other aye-ayes over relatively short geographic distances. For comparison, the average FST value between the North and East aye-aye populations--separated by only 248 km--is over 2.1-times greater than that observed between human Africans and Europeans. This finding is consistent with prior watershed- and climate-based hypotheses of a center of endemism in northern Madagascar. Taken together, these results suggest a strong and long-term biogeographical barrier to gene flow. Thus, the specific attention that should be directed toward preserving large, contiguous aye-aye habitats in northern Madagascar may also benefit the conservation of other distinct taxonomic units. To help facilitate future ecological- and conservation-motivated population genomic analyses by noncomputational biologists, the analytical toolkit used in this study is available on the Galaxy Web site.

Madagascar: A History of Arrivals, What Happened, and Will Happen Next

Most of the ancestors of today's human and animal populations reached Madagascar over the last 65 million years, by a variety of routes at a variety of times. Settlers encountered a big, isolated island with an unpredictable climate and a wide array of landscapes. Although patterns of diversification were driven by different mechanisms in humans and animals, the complex interplay between historical contingency and responsiveness to local conditions is evident in both.

Global climate change will affect Madagascar, although exactly how remains unclear, and the immediate impact of human activity on the island is overtaking that of gradual global change. Three themes in this review bear on the future: the continuing impact of recent, cataclysmic events on modern communities of people, plants, and animals; Madagascar's long and dynamic environmental history; and the complicated history of how people settled and interacted with the island's landscapes. A deeper understanding of all three can contribute to wise decision making in the coming years.

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar

We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ~3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ~2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ~10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage-a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.