Understanding the processes that drive phenotypic diversification and underpin speciation is key to elucidating how biodiversity has evolved. Although these processes have been studied across a wide array of clades, adaptive radiations (ARs), which are systems with multiple closely related species and broad phenotypic diversity, have been particularly fruitful for teasing apart the factors that drive and constrain diversification. As such, ARs have become popular candidate study systems for determining the extent to which ecological features, including aspects of organisms and the environment, and inter- and intraspecific interactions, led to evolutionary diversification. Despite substantial past empirical and theoretical work, understanding mechanistically how ARs evolve remains a major challenge. Here, we highlight a number of understudied components of the environment and of lineages themselves, which may help further our understanding of speciation and AR. We also outline some substantial remaining challenges to achieving a detailed understanding of adaptation, speciation, and the role of ecology in these processes. These major challenges include identifying factors that have a causative impact in promoting or constraining ARs, gaining a more holistic understanding of features of organisms and their environment that interact resulting in adaptation and speciation, and understanding whether the role of these organismal and environmental features varies throughout the radiation process. We conclude by providing perspectives on how future investigations into the AR process can overcome these challenges, allowing us to glean mechanistic insights into adaptation and speciation.

Lemurs are often cited as an example of adaptive radiation, as more than 100 extant species have evolved and filled ecological niches on Madagascar. However, recent work suggests that lemurs lack a hallmark of other adaptive radiations: explosive speciation rates that decline over time. Thus, characterizing the tempo and mode of evolution in lemurs can reveal alternative ways that hyperdiverse clades arise over time, which might differ from traditional models. We explore lemur evolution using a phylogenomic dataset with broad taxonomic sampling that includes the lorisiforms of Asia and continental Africa. Our analyses reveal multiple bursts of diversification (without subsequent declines) that explain much of today's lemur diversity. We also find higher rates of speciation in Madagascar's lemurs compared to lorisiforms, and we demonstrate that the lemur clades with high diversification rates also have high rates of genomic introgression. This suggests that hybridization in these primates is not an evolutionary dead-end, but potential fuel for diversification. Considering the conservation crisis affecting strepsirrhine primates, with approximately 95% of species threatened with extinction, this study offers a perspective for explaining Madagascar's primate diversity and reveals patterns of speciation, extinction, and gene flow that will help inform future conservation decisions.

The gut microbiome is now understood to play essential roles in host nutrition and health and has become a dominant research focus in primatology. Over the past decade, research has clarified the evolutionary traits that govern gut microbiome structure across species and the ecological traits that further influence consortia within them. Nevertheless, we stand to gain resolution by sampling hosts in understudied habitats. We focus on the lemurs of Madagascar's central highlands. Madagascar's highlands have a deep history as heterogeneous grassland-forest mosaics, but due to significant anthropogenic modification, have long been overlooked as lemur habitat. We collected fecal samples from Verreaux's sifakas (Propithecus verreauxi), common brown lemurs (Eulemur fulvus), and Goodman's mouse lemurs (Microcebus lehilahytsara) inhabiting two protected areas in the highlands and used amplicon sequencing to determine gut microbiome diversity and membership. As expected, the lemurs harbored distinct gut consortia tuned to their feeding strategies. Mouse lemurs harbored abundant Bifidobacterium and Alloprevotella that are implicated in gum metabolism, sifakas harbored abundant Lachnospiraceae that are implicated in leaf-fiber metabolism, and brown lemurs harbored diverse consortia with abundant WCBH1-41 that could be associated with frugivory in harsh seasons and habitats. Within brown lemurs, a suite of bacteria varied between seed-packed and leaf-packed feces, a proxy for dietary intakes, collected from the same group over days. Our results underscore the evolutionary and ecological factors that govern primate gut microbiomes. More broadly, we showcase the forests of Madagascar's central highlands as rich habitat for future research of lemur ecology and evolution.

Every mammal studied to date has been found to have a male mutation bias: male parents transmit more de novo mutations to offspring than female parents, contributing increasingly more mutations with age. Although male-biased mutation has been studied for more than 75 years, its causes are still debated. One obstacle to understanding this pattern is its near universality-without variation in mutation bias, it is difficult to find an underlying cause. Here, we present new data on multiple pedigrees from two primate species: aye-ayes (Daubentonia madagascariensis), a member of the strepsirrhine primates, and olive baboons (Papio anubis). In stark contrast to the pattern found across mammals, we find a much larger effect of maternal age than paternal age on mutation rates in the aye-aye. In addition, older aye-aye mothers transmit substantially more mutations than older fathers. We carry out both computational and experimental validation of our results, contrasting them with results from baboons and other primates using the same methodologies. Further, we analyze a set of DNA repair and replication genes to identify candidate mutations that may be responsible for the change in mutation bias observed in aye-ayes. Our results demonstrate that mutation bias is not an immutable trait, but rather one that can evolve between closely related species. Further work on aye-ayes (and possibly other lemuriform primates) should help to explain the molecular basis for sex-biased mutation.

Every mammal studied to date has been found to have a male mutation bias: male parents transmit more de novo mutations to offspring than female parents, contributing increasingly more mutations with age. Although male-biased mutation has been studied for more than 75 years, its causes are still debated. One obstacle to understanding this pattern is its near universality--without variation in mutation bias, it is difficult to find an underlying cause. Here, we present new data on multiple pedigrees from two primate species: aye-ayes (Daubentonia madagascarensis), a member of the strepsirrhine primates, and olive baboons (Papio anubis). In stark contrast to the pattern found across mammals, we find a much larger effect of maternal age than paternal age on mutation rates in the aye-aye. In addition, older aye-aye mothers transmit substantially more mutations than older fathers. We carry out both computational and experimental validation of our results, contrasting them with results from baboons and other primates using the same methodologies. Further, we analyze a set of DNA repair and replication genes to identify candidate mutations that may be responsible for the change in mutation bias observed in aye-ayes. Our results demonstrate that mutation bias is not an immutable trait, but rather one that can evolve between closely related species. Further work on aye-ayes (and possibly other lemuriform primates) should help to explain the molecular basis for sex-biased mutation. ### Competing Interest Statement The authors have declared no competing interest.

Mouse lemurs (genus Microcebus) are a clade of approximately 26 named species of small, nocturnal primates endemic to Madagascar. The genus radiated one to ten million years ago and is morphologically cryptic, with most species having been named within the past 20 years largely based on phylogenetic analysis of short fragments of mitochondrial data. More recent work has been focused on revisiting species designations with autosomal nuclear data using more sophisticated statistical approaches. The order of speciation events in Microcebus remains contentious, particularly with regard to the placement of the M. ravelobensis clade. We investigated support for previous phylogenetic hypotheses based on available whole-genome assemblies from six species and an outgroup. We recovered over 4,000 one-to-one orthologs from these assemblies and used concatenation and coalescent species tree methods to evaluate if differences between previous studies were due to methodological differences or to limitations from too few loci. Observed gene tree discordance was high with patterns inconsistent with incomplete lineage sorting alone. Therefore, we estimated phylogenetic networks to investigate ancient introgression events that may explain observed gene tree distributions and previous phylogenetic conflicts. A network model, invoking some role for introgressive hybridization in the early evolution of Microcebus, better characterizes phylogenetic relationships than does any binary species tree. Our results provide insights into the biogeographic history of a threatened and diverse group of primates while also highlighting an important role for phylogenetic network methods in resolving cases of phylogenetic uncertainty.

Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel’s sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel’s sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.

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. A spatial taxonomic framework integrating genomic, morphological, ecological, life history and acoustic data is used to clarify the cryptic evolution of the taxonomically controversial mouse lemur complex, with a view to aiding future conservation of this and other similarly cryptic clades.

Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Lemurs are a well-known example of adaptive radiation. Since colonizing Madagascar, more than 100 extant lemur species have evolved to fill the variety of ecological niches on the island. However, recent work suggests that lemurs do not exhibit one of the hallmarks of adaptive radiations: explosive speciation rates that decline over time. We test this idea using a phylogenomic dataset with broad taxonomic sampling of lemurs and their sister group, the lorisiforms of Asia and continental Africa. We find higher rates of speciation in Madagascar’s lemurs compared to lorisiforms and we confirm that lemurs did not experience an “early burst” of speciation after colonizing Madagascar. Instead, we identify three independent bursts of speciation approximately 15 million years ago that underly much of today’s lemur diversity. We demonstrate that the lemur clades with exceptionally high diversification rates have higher rates of introgression. This suggests that hybridization in these primates is not an evolutionary dead- end, but a driving force for diversification. Considering the conservation crisis affecting strepsirrhine primates, with approximately 95% of species being threatened with extinction, this phylogenomic study offers a new perspective for explaining Madagascar’s exceptional primate diversity and reveals patterns of speciation, extinction, and gene flow that will help inform future conservation decisions.

House mice, Mus musculus, are highly adapted to anthropogenic spaces. Fecal samples were collected from house mice entering primate enclosure areas at the Duke Lemur Center (Durham, NC, USA). We identified 14 cressdnavirus and 59 microvirus genomes in these mouse feces.

Hibernation is a widespread metabolic strategy among mammals for surviving periods of food scarcity. During hibernation, animals naturally alternate between metabolically depressed torpor bouts and energetically expensive arousals without ill effects. As a result, hibernators are promising models for investigating mechanisms that buffer against cellular stress, including telomere protection and restoration. In non-hibernators, telomeres, the protective structural ends of chromosomes, shorten with age and metabolic stress. In temperate hibernators, however, telomere shortening and elongation can occur in response to changing environmental conditions and associated metabolic state. We investigate telomere dynamics in a tropical hibernating primate, the fat-tailed dwarf lemur ( Cheirogaleus medius ). In captivity, these lemurs can hibernate when maintained under cold temperatures (11–15 °C) with limited food provisioning. We study telomere dynamics in eight fat-tailed dwarf lemurs at the Duke Lemur Center, USA, from samples collected before, during, and after the hibernation season and assayed via qPCR. Contrary to our predictions, we found that telomeres were maintained or even lengthened during hibernation, but shortened immediately thereafter. During hibernation, telomere lengthening was negatively correlated with time in euthermia. Although preliminary in scope, our findings suggest that there may be a preemptive, compensatory mechanism to maintain telomere integrity in dwarf lemurs during hibernation. Nevertheless, telomere shortening immediately afterward may broadly result in similar outcomes across seasons. Future studies could profitably investigate the mechanisms that offset telomere shortening within and outside of the hibernation season and whether those mechanisms are modulated by energy surplus or crises.

The dwarf lemurs (Cheirogaleus spp.) of Madagascar are the only obligate hibernators among primates. Despite century-old field accounts of seasonal lethargy, and more recent evidence of hibernation in the western fat-tailed dwarf lemur (Cheirogaleus medius), inducing hibernation in captivity remained elusive for decades. This included the Duke Lemur Center (DLC), which maintains fat-tailed dwarf lemurs and has produced sporadic research on reproduction and metabolism. With cumulative knowledge from the field, a newly robust colony, and better infrastructure, we recently induced hibernation in DLC dwarf lemurs. We describe two follow-up experiments in subsequent years. First, we show that dwarf lemurs under stable cold conditions (13°C) with available food continued to eat daily, expressed shallower and shorter torpor bouts, and had a modified gut microbiome compared to peers without food. Second, we demonstrate that dwarf lemurs under fluctuating temperatures (12-30°C) can passively rewarm daily, which was associated with altered patterns of fat depletion and reduced oxidative stress. Despite the limitations of working with endangered primates, we highlight the promise of studying hibernation in captive dwarf lemurs. Follow-up studies on genomics and epigenetics, metabolism, and endocrinology could have relevance across multidisciplinary fields, from biomedicine to evolutionary biology, and conservation.

Societal Impact Statement Recognizing Loudetia ‐dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component of Madagascar's biodiversity. A better understanding of the plant species that form grassland ecosystems is necessary for effective land management strategies that support livelihoods, but substantial financial and logistical barriers exist to implementing conservation genetic studies using contemporary genomic tools. Some challenges for population genetic analyses of non‐model polyploids lacking reference genomes can be ameliorated by developing computational resources that leverage a cost‐effective data generation strategy that requires no prior genetic knowledge of the target species. This may benefit conservation programs with small operating budgets while reducing uncertainty compared to status quo microsatellite assays. Summary The extent of Madagascar's grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C 4 fire‐adapted grass, Loudetia simplex , as a proxy for estimating grassland change through time. We carefully examined the utility of target‐enrichment data for population genetics to make recommendations for conservation genetics. We explored the potential of estimating individual ploidy levels from target‐enrichment data and how assumptions about ploidy could affect analyses. We developed a novel bioinformatic pipeline to estimate ploidy and genotypes from target‐enrichment data. We estimated standard population genetic summary statistics in addition to species trees and population structure. Extended Bayesian skyline plots provided estimates of population size through time for empirical and simulated data. All Malagasy L. simplex individuals sampled in this study formed a clade and possibly indicated an ancestral Central Highland distribution of 800 m in altitude and above. Demographic models suggested grassland expansions occurred prior to the Last Interglacial Period and supported extensive grasslands prior to human colonization. Though there are limitations to target‐enrichment data for population genetic studies, we find that analyses of population structure are reliable. Genetic variation in L. simplex supports widespread grasslands in Madagascar prior to the more recent periods of notable paleoclimatic change. However, the methods explored here could not differentiate between paleoclimatic change near the Last Glacial Maximum and anthropogenic effects. Target‐enrichment data can be a valuable tool for analyses of population structure in the absence a reference genome.

The Papillomaviridae are a family of vertebrate-infecting viruses of oncogenic potential generally thought to be host species- and tissue-specific. Despite their phylogenetic relatedness to humans, there is a scarcity of data on papillomaviruses (PVs) in speciose non-human primate lineages, particularly the lemuriform primates. Varecia variegata (black-and-white ruffed lemurs) and Varecia rubra (red ruffed lemurs), two closely related species comprising the Varecia genus, are critically endangered with large global captive populations. Varecia variegata papillomavirus (VavPV) types −1 and −2, the first PVs in lemurs with a fully identified genome, were previously characterized from captive V. variegata saliva. To build upon this discovery, saliva samples were collected from captive V. rubra with the following aims: (1) to identify PVs shared between V. variegata and V. rubra and (2) to characterize novel PVs in V. rubra to better understand PV diversity in the lemuriform primates. Three complete PV genomes were determined from V. rubra samples. Two of these PV genomes share 98% L1 nucleotide identity with VavPV2, denoting interspecies infection of V. rubra by VavPV2. This work represents the first reported case of interspecies PV infection amongst the strepsirrhine primates. The third PV genome shares <68% L1 nucleotide identity with that of all PVs. Thus, it represents a new PV species and has been named Varecia rubra papillomavirus 1 (VarPV1). VavPV1, VavPV2, and VarPV1 form a new clade within the Papillomaviridae family, likely representing a novel genus. Future work diversifying sample collection (i.e., lemur host species from multiple genera, sample type, geographic location, and wild populations) is likely to uncover a world of diverse lemur PVs.

Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1000 transcriptome loci from 14 species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling. [divergence time; gene flow; hybridization; introgression; MSci model; multispecies coalescent].

The diversity of viruses identified from the various niches of the human oral cavity—from saliva to dental plaques to the surface of the tongue—has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).

1. Research Aims — The extent of Madagascar’s grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C4 fire-adapted grass, Loudetia simplex , as a proxy for estimating grassland change through time. We carefully examined the utility of target-enrichment data for population genetics to make recommendations for conservation genetics. We explored the potential of estimating individual ploidy levels from target-enrichment data and how assumptions about ploidy could affect analyses.2. Methods — We developed a novel bioinformatic pipeline to estimate ploidy and genotypes from target-enrichment data. We estimated standard population genetic summary statistics in addition to species trees and population structure. Extended Bayesian skyline plots provided estimates of population size through time for empirical and simulated data.3. Key Result — All Malagasy Loudetia simplex individuals sampled in this study formed a clade and possibly indicated an ancestral Central Highland distribution of 800m in altitude and above. Demographic models suggested grassland expansions occurred prior to the Last Interglacial Period and supported extensive grasslands prior to human colonization. Though there are limitations to target-enrichment data for population genetic studies, we find that analyses of population structure are reliable.4. Key Point —Genetic variation in Loudetia simplex supports widespread grasslands in Madagascar prior to the more recent periods of notable paleoclimatic change. However, the methods explored here could not differentiate between paleoclimatic change near the Last Glacial Maximum and anthropogenic effects. Target-enrichment data can be a valuable tool for analyses of population structure in the absence a reference genome.Societal Impact Statement Recognizing Loudetia dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component of Madagascar’s biodiversity. Urgently required are biodiversity inventories and integrative taxonomic treatments of grassland flora and fauna to asses risks to understudied ecosystems historically regarded as wastelands. Substantial financial and logistical barriers exist to implementing conservation studies using contemporary genomic tools. We ameliorated some of the challenges for population genetic analyses of non-model polyploids lacking reference genomes by developing computational resources to leverage a cost-effective data generation strategy that requires no prior genetic knowledge of the target species.Résumé 1. Les objectifs de la recherche — L’étendue des écosystèmes ouverts de Madagascar avant la colonisation humaine reste à éclaircir. Nous avons utilisé une analyse de la population génétique d’une graminée C4 adaptée au feu, largement dominante, Loudetia simplex, comme référence pour estimer les changements au niveau de ces biomes au fil du temps. Nous avons examiné attentivement l’utilité des données d’enrichissement ciblé pour la génétique de population afin de formuler des recommandations pour la conservation génétique. Nous avons exploré le potentiel de l’estimation du niveau des ploidies individuelles à partir des données d’enrichissement ciblé et comment les hypothèses à propos de ces ploidies pourraient affecter les analyses.2. Les méthodes — Nous avons développé un nouveau canal bioinformatique pour estimer les ploidies et les génotypes à partir des données d’enrichissement ciblé. Nous avons estimé les statistiques standard de la population génétique, en plus des arbres des espèces et de la structure de la population. L’utilisation des tracés étendus du ciel bayésien a fourni une estimation de la taille de la population au fil du temps pour des données empiriques et simulées.3. Résultat clé — Tous les individus Malagasy de Loudetia simplex échantillonnés dans cette étude ont formé un clade, indiquant une éventuelle ancienne distribution dans les hauts plateaux. Les modèles démographiques suggèrent une expansion des prairies bien avant la dernière période interglaciaire et soutiennent l’existence d’une vaste distribution avant la colonisation humaine. Bien qu’il y ait des limites à l’enrichissement des données cibles pour l’étude de la génétique des populations, nous constatons que l’analyse des structures des populations est fiable.4. Les points clés — La variation génétique de Loudetia simplex soutient l’existence de vastes prairies à Madagascar avant les périodes plus récentes de changements paléoclimatiques notables. Cependant, les méthodes explorées ici n’ont pas permis de faire la différence entre les changements paléoclimatiques près du dernier maximum glaciaire et les effets anthropogènes. Les données d’enrichissement ciblé peuvent être un outil précieux pour les analyses de la structure des populations en l’absence d’un génome de référence.Déclaration d’impact societal Reconnaître que les prairies dominées par Loudetia étaient répandues avant la colonisation humaine souligne que les écosystèmes ouverts étaient et continuent d’être un composant important de la biodiversité de Madagascar. Il est urgent de réaliser des inventaires de la biodiversité et une taxonomie intégrée pour le traitement de la flore et de la faune des écosystèmes ouverts afin d’évaluer les risques pour les écosystèmes sous-étudiés considérés historiquement comme des terres en friches. Des barrières financières et logistiques existent pour mettre en œuvre l’étude de la conservation en utilisant les outils génomiques contemporains. Nous avons amélioré certains des défis liés aux analyses génétiques de populations de polyploïdes non modèles, sans génomes de référence, en développant des ressources informatiques pour exploiter une stratégie pouvant générer des données rentables ne nécessitant aucune connaissance génétique préalable de l’espèce cible.Famintinana 1. Ny tanjon’ny fikarohana — Mbola tsy fantatra mazava tsara ny fivelaran’ny hivoka teto Madagasikara talohan’ny fahatongava’ny olombelona. Mba ahafantarana ny fihovana nitranga nandritra ny fotoana naharitra teo amin’ireo hivoka ireo dia nanao famakafakahana ara-genetika amin’ny ahitra C4 miompana amin’ny afo iray antsoina Loudetia simplex ara-tsiantifika na Berambo na Hara amin’ny teny malagasy izahay. Nandinika tsara ny maha-zava-dehibe ny fampitomboana ny antotan-kevitra mba ahafahana manolo-kevitra momba ny fiarovana ny fototarazo genetika. Nandinika ny mety mampiavaka ny fanombanana an’ny ploidy tsirairay amin’ny fampitomboana antotan-kevitra sy ny mety ho fiantraikan’ny fiheverana momba ireo ploidy ireo amin’ny fikarohana.2. Fomba Fiasa — Namorona fantsona bioinformatika vaovao mba ahafahana manombana ny ploidy sy ny « genotypes » avy amin’ny antotan-kevitra nokendrena izahay. Notombanana ny antontan’isa famintinana ny fototarazo ara-genetikan’ireo vondron’ahitra ireo, miampy ny karazana hazo sy ny firafitry ny vondrona na koa hoe mponina. Nanome tombantombana ny haben’ny mponina amin’ny alàlan’ny fotoana ny antontan-kevitra voavinavina azo tamin’ny fikarohana. Fikarohana izay azo tamin’ny alalan’ny « Bayesina Skuline Plots ».3. Vokam-pikarohana fototra — Ny vondrona Loudetia simplex eto Madagasikara izay niasana dia namorona « clade » na fikambanana iray, izay manondro ny mety maha ela netezana sy tranainy an’io ahitra io eny amin’ny faritra avo. Ny modely demografika dia manoro hevitra amin’ny naha be velarana ny hivoka izay efa ela talohan’ny vanim-potoana « interglacial » farany ary manohana ny fivelarana midadasika an’ireo kijana ireo alohan’ny fonenan’ny olombelona. Na dia misy fetrany aza ny fampitomboana ny antotan-kevitra kendrena amin’ny fandalinana ny fototarazo genetika momban’ny mponina, dia hita fa azo itokisana ny fikarohana natao momban’ny firafitry ny mponina.4. Hevi-dehibe — Ny fahasamihafana ara-genetika ao amin’ny Loudetia simplex dia manohana ny fisian’ny hivoka na kijana midadasika eto Madagasikara talohan’ny vanim-potoanan’ny fiovana paleoclimatika nisongadina. Na izany aza, ny fombam-pikarohana nampiasana teto dia tsy nahavita nanavaka ny fiovan’ny paleoclimatika akaikin’ny vanim-potoana lehibe nangatsiaka farany sy ny vokatry ny fitrandrahana nataon’ny olombelona. Mety ho fitaovana manan-danja amin’ny famakafakana ny firafitry ny mponina ny antotan-kevitra nampitombona na dia tsy misy fitaovana genomika iangaina aza.Fanambarana fiantraika ara-tsosialy Ny fanekena fa niely patrana ny hivoka itoeran’ny Loudetia talohan’ny fanjanahan’ny olombelona dia manamarika fa ireo hivoka ireo dia singa manan-danja amin’ny zavamananaina eto Madagasikara. Ilaina maika ny fahafantarana ara biolojika sy taxononomique ny zavamaniry sy ny biby amin’ny hivoka mba hanombanana ny loza mety hitranga amin’ny hivoka izay tsy ananana fahalalana maro sady heverina ho tany maina. Misy sakana ara-bola sy ara-pitaovana amin’ny fampiharana ny fandalinana momba ny fiarovana izay nampiasana fitaovana génomika ankehitriny. Nohatsarainay ny sasany amin’ireo fanamby mifandraika amin’ny famakafakana ara-genetika ny mponina manana ploidy maro tsy modely, izay tsy misy fitaovana genomika iaingana, amin’ny alàlan’ny fampivoarana loharanon-kevitra kajy mba hitrandrahana paikady izay mety hiteraka angon-drakitra mahomby tsy mitaky fahalalana mahakasika ny fototarazo ara-genetika ny zava-maniry izay tiana karohina.### Competing Interest StatementThe authors have declared no competing interest.