Past environmental changes affected lemur population dynamics prior to human impact in Madagascar

Species-Specific Traits Shape Genetic Diversity During an Expansion-Contraction Cycle and Bias Demographic History Reconstruction

Species ranges are dynamic, experiencing expansions, contractions or shifts in response to habitat changes driven by extrinsic factors such as climate change or human activities. While existing research examines the genetic consequences of spatial processes, few studies integrate species-specific traits to analyse how habitat changes affect co-existing species. In this study, we address this gap by investigating how genetic diversity patterns vary among species with different traits (such as generation length, population density and dispersal) experiencing similar habitat changes. Using spatial simulations and a simpler panmictic population model, we investigate the temporal genetic diversity in refugium populations undergoing range expansion of their habitat, followed by stationary and contraction periods. By varying habitat contraction speed and species traits, we identified three distinct temporal dynamics of genetic diversity during contraction: (i) a decrease in genetic diversity, (ii) an initial increase followed by a decrease and (iii) a continuous increase throughout the contraction period. We show that genetic diversity trajectories during population decline can be predicted by comparing sampled population diversity to equilibrium values expected under expanded and contracted habitat ranges. Our study also challenges the belief that high genetic diversity in a refugium population is due to a recent and rapid habitat loss. Instead, we found contrasting effects of contraction speed on genetic diversity depending on the interaction between species-specific traits and the dynamics of habitat change. Finally, using simulated genetic data, we found that demographic histories inferred from effective population size estimates may vary across species, even when they experience similar habitat changes.

Integrative taxonomy clarifies the evolution of a cryptic primate clade

Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar's biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation by distance. We systematically apply this framework to an entire taxonomically controversial primate clade, the mouse lemurs (genus Microcebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis within the genus is best explained by a model of morphological stasis imposed by stabilizing selection and a neutral process of niche diversification. Finally, by clarifying species limits and defining evolutionarily significant units, we provide new conservation priorities, bridging fundamental and applied objectives in a generalizable framework.

Effects of Social Structure on Effective Population Size Change Estimates

Most methods currently used to infer the "demographic history of species" interpret this expression as a history of population size changes. The detection, quantification, and dating of demographic changes often rely on the assumption that population structure can be neglected. However, most vertebrates are typically organized in populations subdivided into social groups that are usually ignored in the interpretation of genetic data. This could be problematic since an increasing number of studies have shown that population structure can generate spurious signatures of population size change. Here, we simulate microsatellite data from a species subdivided into social groups where reproduction occurs according to different mating systems (monogamy, polygynandry, and polygyny). We estimate the effective population size (N e) and quantify the effect of social structure on estimates of changes in N e. We analyze the simulated data with two widely used methods for demographic inference. The first approach, BOTTLENECK, tests whether the samples are at mutation-drift equilibrium and thus whether a single N e can be estimated. The second approach, msvar, aims at quantifying and dating changes in N e. We find that social structure may lead to signals of departure from mutation-drift equilibrium including signals of expansion and bottlenecks. We also find that expansion signals may be observed under simple stationary Wright-Fisher models with low diversity. Since small populations tend to characterize many endangered species, we stress that methods trying to infer N e should be interpreted with care and validated with simulated data incorporating information about structure. Spurious expansion signals due to social structure can mask critical population size changes. These can obscure true bottleneck events and be particularly problematic in endangered species.

Montane rainforest dynamics under changes in climate and human impact during the past millennia in northern Madagascar

Although it is well known that humans substantially altered the Malagasy ecosystems, the timing of the human arrival as well as the extension of their environmental impact is yet not well understood. This research aims to study the influence of early human impact and climate change on rainforests and wildlife in northern Madagascar during the past millennia. Results obtained from the lake sediment in a montane environment showed significant changes in vegetation within the lake catchment associated with a major drought that started approximately 1100 years ago. Human impact, revealed by fires, began at roughly the same time and occurred outside the lake catchment. Although this does not dismiss the impacts that humans had at a regional scale, this result demonstrates that the late Holocene natural drought also significantly impacted the ecosystems independently of anthropogenic activities. At a regional scale, a review of species demographic history revealed a substantial number of population bottlenecks during the last millennia, probably resulting from this combination of human-related impact and natural climate changes. This research highlights the importance of a multi-site and multi-proxy comparison for deciphering the nature and succession of environmental changes.

Zonal control on Holocene precipitation in northwestern Madagascar based on a stalagmite from Anjohibe

The Malagasy Summer Monsoon is an important part of the larger Indian Ocean and tropical monsoon region. As the effects of global warming play out, changes to precipitation in Madagascar will have important ramifications for the Malagasy people. To help understand how precipitation responds to climate changes we present a long-term Holocene speleothem record from Anjohibe, part of the Andranoboka cave system in northwestern Madagascar. To date, it is the most complete Holocene record from this region and sheds light on the nature of millennial and centennial precipitation changes in this region. We find that over the Holocene, precipitation in northwestern Madagascar is actually in phase with the Northern Hemisphere Asian monsoon on multi-millennial scales, but that during some shorter centennial-scale events such as the 8.2 ka event, Anjohibe exhibits an antiphase precipitation signal to the Northern Hemisphere. The ultimate driver of precipitation changes across the Holocene does not appear to be the meridional migration of the monsoon. Instead, zonal sea surface temperature gradients in the Indian Ocean seem to play a primary role in precipitation changes in northwestern Madagascar.

Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts

Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.

The importance of well protected forests for the conservation genetics of West African colobine monkeys

In tropical forests, anthropogenic activities are major drivers of the destruction and degradation of natural habitats, causing severe biodiversity loss. African colobine monkeys (Colobinae) are mainly folivore and strictly arboreal primates that require large forests to subsist, being among the most vulnerable of all nonhuman primates. The Western red colobus Piliocolobus badius and the King colobus Colobus polykomos inhabit highly fragmented West African forests, including the Cantanhez Forests National Park (CFNP) in Guinea-Bissau. Both species are also found in the largest and best-preserved West African forest-the Taï National Park (TNP) in Ivory Coast. Colobine monkeys are hunted for bushmeat in both protected areas, but these exhibit contrasting levels of forest fragmentation, thus offering an excellent opportunity to investigate the importance of well-preserved forests for the maintenance of evolutionary potential in these arboreal primates. We estimated genetic diversity, population structure, and demographic history by using microsatellite loci and mitochondrial DNA. We then compared the genetic patterns of the colobines from TNP with the ones previously obtained for CFNP and found contrasting genetic patterns. Contrary to the colobines from CFNP that showed very low genetic diversity and a strong population decline, the populations in TNP still maintain high levels of genetic diversity and we found no clear signal of population decrease in Western red colobus and a limited decrease in King colobus. These results suggest larger and historically more stable populations in TNP compared to CFNP. We cannot exclude the possibility that the demographic effects resulting from the recent increase of bushmeat hunting are not yet detectable in TNP using genetic data. Nevertheless, the fact that the TNP colobus populations are highly genetically diverse and maintain large effective population sizes suggests that well-preserved forests are crucial for the maintenance of populations, species, and probably for the evolutionary potential in colobines.

Cutmarked bone of drought-tolerant extinct megafauna deposited with traces of fire, human foraging, and introduced animals in SW Madagascar

People could have hunted Madagascar's megafauna to extinction, particularly when introduced taxa and drought exacerbated the effects of predation. However, such explanations are difficult to test due to the scarcity of individual sites with unambiguous traces of humans, introduced taxa, and endemic megaherbivores. We excavated three coastal ponds in arid SW Madagascar and present a unique combination of traces of human activity (modified pygmy hippo bone, processed estuarine shell and fish bone, and charcoal), along with bones of extinct megafauna (giant tortoises, pygmy hippos, and elephant birds), extirpated fauna (e.g., crocodiles), and introduced vertebrates (e.g., zebu cattle). The disappearance of megafauna from the study sites at ~ 1000 years ago followed a relatively arid interval and closely coincides with increasingly frequent traces of human foraging, fire, and pastoralism. Our analyses fail to document drought-associated extirpation or multiple millennia of megafauna hunting and suggest that a late combination of hunting, forest clearance, and pastoralism drove extirpations.

RADseq Data Suggest Occasional Hybridization between Microcebus murinus and M. ravelobensis in Northwestern Madagascar

The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, thereby creating limited opportunity for natural hybridization. This study examines RADseq data from 480 individuals to investigate whether the recent expansion of Microcebus murinus towards the northwest and subsequent secondary contact with Microcebus ravelobensis has resulted in the occurrence of hybridization between the two species. Admixture analysis identified one individual with 26% of nuclear admixture, which may correspond to an F2- or F3-hybrid. A composite-likelihood approach was subsequently used to test the fit of alternative phylogeographic scenarios to the genomic data and to date introgression. The simulations yielded support for low levels of gene flow (2Nm0 = 0.063) between the two species starting before the Last Glacial Maximum (between 54 and 142 kyr). Since M. murinus most likely colonized northwestern Madagascar during the Late Pleistocene, the rather recent secondary contact with M. ravelobensis has likely created the opportunity for occasional hybridization. Although reproductive isolation between these distantly related congeners is not complete, it is effective in maintaining species boundaries.

Rain Forest Fragmentation and Environmental Dynamics on Nosy Be Island (NW Madagascar) at 1300 cal BP Is Attributable to Intensified Human Impact

Madagascar houses one of the Earth’s biologically richest, but also one of most endangered, terrestrial ecoregions. Although it is obvious that humans substantially altered the natural ecosystems during the past decades, the timing of arrival of early inhabitants on Madagascar as well as their environmental impact is still intensively debated. This research aims to study the beginning of early human impact on Malagasy natural ecosystems, specifically on Nosy Be island (NW Madagascar) by targeting the sedimentary archive of Lake Amparihibe, an ancient volcanic crater. Based on pollen, fungal spore, other non-pollen palynomorph, charcoal particle and diatom analyses combined with high-resolution sediment-physical and (in)organic geochemical data, paleoenvironmental dynamics during the past three millennia were reconstructed. Results indicate a major environmental change at ca. 1300 cal BP characterized by an abrupt development of grass (C4) dominated and fire disturbed landscape showing the alteration of natural rain forest. Further, increased soil erodibility is suggested by distinct increase in sediment accumulation rates, a strong pulse of nutrient input, higher water turbidity and contemporaneous increase in spores of mycorrhizal fungi. These parameters are interpreted to show a strong early anthropogenic transformation of the landscape from rain forest to open grassland. After ca. 1000 cal BP, fires remain frequent and vegetation is dominated by forest/grassland mosaic. While natural vegetation should be dominated by rain forest on Nosy Be, these last results indicate that human continuously impacted the landscapes surrounding the lake. At a local scale, our data support the “subsistence shift hypothesis” which proposed that population expansion with development of herding/farming altered the natural ecosystems. However, a precise regional synthesis is challenging, since high-resolution multi-proxy records from continuous sedimentary archives as well as records located further north and in the hinterland are still scarce in Madagascar. The lack of such regional synthesis also prevents precise comparison between different regions in Madagascar to detect potential (dis)similarities in climate dynamics, ecosystem responses and anthropogenic influences at the island’s scale during the (late) Holocene.

Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar

BACKGROUND

Quaternary climate fluctuations have been acknowledged as major drivers of the geographical distribution of the extraordinary biodiversity observed in tropical biomes, including Madagascar. The main existing framework for Pleistocene Malagasy diversification assumes that forest cover was strongly shaped by warmer Interglacials (leading to forest expansion) and by cooler and arid glacials (leading to forest contraction), but predictions derived from this scenario for forest-dwelling animals have rarely been tested with genomic datasets.

RESULTS

We generated genomic data and applied three complementary demographic approaches (Stairway Plot, PSMC and IICR-simulations) to infer population size and connectivity changes for two forest-dependent primate species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. The analyses suggested major demographic changes in both species that could be interpreted in two ways, depending on underlying model assumptions (i.e., panmixia or population structure). Under panmixia, the two species exhibited larger population sizes across the Last Glacial Maximum (LGM) and towards the African Humid Period (AHP). This peak was followed by a population decline in M. ravelobensis until the present, while M. murinus may have experienced a second population expansion that was followed by a sharp decline starting 3000 years ago. In contrast, simulations under population structure suggested decreasing population connectivity between the Last Interglacial and the LGM for both species, but increased connectivity during the AHP exclusively for M. murinus.

CONCLUSION

Our study shows that closely related species may differ in their responses to climatic events. Assuming that Pleistocene climatic conditions in the lowlands were similar to those in the Malagasy highlands, some demographic dynamics would be better explained by changes in population connectivity than in population size. However, changes in connectivity alone cannot be easily reconciled with a founder effect that was shown for M. murinus during its colonization of the northwestern Madagascar in the late Pleistocene. To decide between the two alternative models, more knowledge about historic forest dynamics in lowland habitats is necessary. Altogether, our study stresses that demographic inferences strongly depend on the underlying model assumptions. Final conclusions should therefore be based on a comparative evaluation of multiple approaches.