Papers by Cynthia Frasier
Oryx, May 16, 2023
Anthropogenic activities are negatively affecting the flora and fauna of Madagascar, including it... more Anthropogenic activities are negatively affecting the flora and fauna of Madagascar, including its Endangered flagship lemur species, the ring-tailed lemur Lemur catta. Population numbers at some sites are rapidly declining, yet much of the species' habitat is insufficiently surveyed. Because widespread population assessments are critical to guiding conservation management strategies, additional data are needed to monitor L. catta population trends and to identify the limits of their geographical range. Here we report survey results confirming the presence of this species at of sites in southern and southwestern Madagascar, including three subpopulations that were previously considered likely to be locally extinct. We identified a minimum of L. catta individuals (summing only maximum group sizes at each site) and as many as , individuals (using estimated population counts). These findings help refine the distribution of L. catta and reaffirm their presence in areas of their historical geographical range. Identifying species occupancy at sites such as these provides valuable data to support species conservation, but also highlights the need for additional surveys throughout the range of the species.
International Journal of Ecology, 2013
A reforestation effort in Kianjavato Commune in southeast Madagascar is presented that combines n... more A reforestation effort in Kianjavato Commune in southeast Madagascar is presented that combines native diversity with rapidly growing introduced and native pioneer trees. This work utilizes a three-tiered corridor design that capitalizes on the region's mountainous terrain. The process of seed selection, transplantation, and survival rate of seedlings over a 16 month period is reported. The uppermost 50% of each mountain is planted with 38 woody species and most closely approximates native forest. This tier was divided into two categories, pioneer and secondary species. Most of the pioneer species were not native; however, results showed that four fast-growing, environmentally-tolerant native species could be suitable alternatives: Streblus mauritianus, Syzygium bernieri, Treculia madagascariensis and Uapaca thouarsii. More than 70,000 seeds of secondary species were extracted from fecal samples from wild, free-ranging black and white ruffed lemurs; the majority of which germinated significantly better after gut passage. The most effective pretreatment that enhanced germination was to scarify unwashed seeds. Commercially valuable trees, belonging to the community members, were grown on the lower half of each mountain. Lastly, the various contributions of the community are described along with agroforestry development plans designed to reduce pressure on forest resources and generate supplemental income.
Botanical Journal of the Linnean Society, Jun 8, 2023
Clarifying generic circumscriptions within Oleaceae improves its complicated infrafamilial classi... more Clarifying generic circumscriptions within Oleaceae improves its complicated infrafamilial classification. Focusing on the small and disjunctly-distrubted subtribe Schreberinae, we use phylogenomic data from plastid and nuclear DNA from an extensive sampling to assess its phylogenetic patterns and biogeographic history. Results show paraphyly among its members, with Comoranthus nested within Schrebera, leading us to synonymize these genera. Schrebera s.l. occurs in four major regions of the world, but its center of origin remains uncertain with three possible ancestral ranges identified. However, the diversification of this genus is estimated to have started in the Early Oligocene (ca. 34 Mya), and its current distribution pattern is best explained by dispersal between landmasses rather than continental vicariance. Madagascar is the center of diversity of Schrebera s.l., where ten endemic species, of which five are new, were recovered from analyses of morphological, molecular, and ecoclimatic data. Therefore, a taxonomic treatment of the species from Madagascar and the Comoro Islands is presented. As currently circumscribed, Schrebera s.l., and thus the monotypic subtribe, includes 16 species (one in South America, two in Southeast Asia, three in Africa, of which one is shared with Madagascar, and 11 in Madagascar and the Comoro Islands).
Journal of Heredity, May 10, 2013
Conservation Genetics, Nov 19, 2019
The critically endangered ploughshare tortoise, Astrochelys yniphora, is endemic to the Baly Bay ... more The critically endangered ploughshare tortoise, Astrochelys yniphora, is endemic to the Baly Bay region of western Madagascar. In 2015, the wild population was estimated to be < 500 subadults/adults across a fragmented habitat, with subsequent field surveys reporting a further decline to a perilously low number of adult tortoises. The primary cause of this decline was poaching for the illegal international pet trade, which has escalated since 2006 leading to the extirpation of ploughshare tortoises from at least two localities. Seizures of smuggled tortoises increased over this same period, with most confiscated animals being incorporated into assurance populations. This study presents a genetic reference, including samples from the extirpated localities. Mitochondrial sequence data and 25 nuclear microsatellite markers were utilized to estimate genetic diversity of the wild population prior to a > 50% decline, identify Management Units (MUs), and present a dataset to assign confiscated individuals to their subpopulation of origin. Despite a long history of exploitation, heterozygosity appeared healthy, ranging from 0.612 to 0.758 across four localities, and no recent genetic bottlenecks were observed. In contrast, the Western Complex, consisting of the Ambatomainty, Andrafiafaly, and Andranolava regions, exhibited a possible decline in allelic diversity. Four genetic clusters were recovered and used to define three MUs corresponding to the following localities: Cap Sada, Beheta, and a combined Western Complex plus Betainalika. Results are discussed in the context of conservation genetic management advising that MUs be treated as conservation units for wild and captive management to maintain the breadth of genetic diversity present in the wild.
Folia Primatologica, Mar 1, 2022
The role of folivorous primates in ecosystem restoration has been largely overlooked. This may pr... more The role of folivorous primates in ecosystem restoration has been largely overlooked. This may primarily be due to the lack of basic ecological information on many of these species. The northern sportive lemur (Lepilemur septentrionalis), for example, is one of the most endangered primates in the world, yet we lack baseline ecological knowledge of this lemur. This dearth only serves to exacerbate their situation as conservation initiatives do not have the fundamental information needed to properly manage conservation efforts for this species. To obtain an ecological baseline for L. septentrionalis, we used instantaneous focal animal sampling to collect behavioral data, including strata use, to investigate feeding ecology for five individuals over a 12-month period (December 2018-November 2019) in Montagne des Français. We conducted a total of 755.1 hours of observation. Our results showed that L. septentrionalis’ diet consisted of mature and young leaves, ripe and unripe fruits, flowers, and buds. Mature leaves of Tamarindus indica were the most frequently consumed resource, yet L. septentrionalis consumed 61 different species of plants from 23 families. Though mature leaves were the most frequently consumed resource overall, we only observed L. septentrionalis eating them during the cold/dry season. The most frequently used stratum during feeding was the canopy, which correlated strongly with the consumption of mature and young leaves. Though many aspects of this species’ diet are similar to other Lepilemur, there are specific ecological conditions, notably seasonal frugivory, which should be considered when developing restoration ecology programs in Montagne des Français.
Folia Primatologica, Feb 14, 2018
Previous studies found that aye-ayes (Daubentonia madagascariensis) consume a variety of non-inve... more Previous studies found that aye-ayes (Daubentonia madagascariensis) consume a variety of non-invertebrate resources, supporting the hypothesis that aye-ayes are too large-bodied to focus feeding efforts on insects. However, these conclusions were based on introduced populations, with little known about aye-aye behaviour and ecology in its natural habitat. This study investigates activity budgets, diet, and home range/territories of 2 male aye-ayes in the Kianjavato Classified Forest, a disturbed forest in southeastern Madagascar, from October 2013 to October 2014. We used radiotelemetry and focal-animal sampling methods to collect behavioural data. We recorded GPS coordinates of the focal animal every 20 min, calculating the home range size for each individual. Results showed that male aye-ayes spent most of their time feeding and travelling. Their feeding time primarily focussed on larvae and adult insects from various substrates, and to a lesser extent Canarium spp. seeds. Home range sizes of the 2 males varied between individuals, overlapped greatly, and appeared to be related to the location of females. Our findings indicate that aye-aye behaviours are strongly indicative of insect-centric feeding ecology.
BMC Genomics, Jun 8, 2018
Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is... more Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19 k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km 2 , while the contemporary distribution is only~1700 km 2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations.
Journal of Heredity, Oct 3, 2016
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently desc... more The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species' boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.
Reptiles & Amphibians
Copyright is held by the authors. Articles in R&A are made available under a Creative Commons Att... more Copyright is held by the authors. Articles in R&A are made available under a Creative Commons Attribution-NonCommercial 4.0 International license. T he current era is described as the sixth extinction event (Purvis et al. 2000) driven by land use change and overexploitation (Hilton-Taylor 2000), with hunting a major anthropogenic driver of biodiversity loss (Bennett et al. 2007). This biodiversity crisis does not spare reptile populations, such as chelonians, the oldest reptile group (Bonin et al. 1998). Slow, not very aggressive, easy to capture, and providing abundant meat, oil, and fat, chelonians have been and still are a source of food in much of the world (Bonin et al. 1998). Since 1600, 11 species of tortoises have become extinct due to slaughter for meat (Honegger 1980). Indeed, 51.9% of the categorized global chelonian diversity is considered threatened (CR + EN + VU), making chelonians the second most threatened vertebrate taxa on the planet after primates (Rhodin et al. 2018). Madagascar counts nine native chelonian species, with five of them endemic (Pedrono 2008), including the Radiated Tortoise, Astrochelys radiata (Shaw 1802), in the southern dry spiny thicket (Glaw and Vences 2007). Primary threats facing this species include high levels of poaching associated with the local bush meat trade and habitat loss (Raxworthy and Nussbaum 2000; Rioux Paquette et al. 2009; Walker et al. 2014; Ganzhorn et al. 2015; Manjoazy et al. 2017). As intense as habitat degradation is in some areas, the main threat to the persistence of the Radiated Tortoise is overexploitation (O'Brien 2002). Radiated Tortoises are extensively collected for food and the local, national, and international pet trade (O'Brien et al. 2003). The people of southwest Madagascar appreciate the tortoise meat during the Christmas and Easter holidays, with another peak of consumption thought to coincide with Independence Day (Pedrono et al. 2000; Manjoazy et al. 2017). Since 1975, increasing demand for tortoise meat and derived products on the international market resulted in the species being listed on Appendix I of CITES. The status of the species continues to deteriorate, and the IUCN Red List classifies the Radiated Tortoise as "Critically Endangered" (Leuteritz and Rioux Paquette 2013), possibly becoming extinct in twenty years (Hudson 2013).
HAL (Le Centre pour la Communication Scientifique Directe), Feb 1, 2023
Folia Primatologica, 2022
The role of folivorous primates in ecosystem restoration has been largely overlooked. This may pr... more The role of folivorous primates in ecosystem restoration has been largely overlooked. This may primarily be due to the lack of basic ecological information on many of these species. The northern sportive lemur (Lepilemur septentrionalis), for example, is one of the most endangered primates in the world, yet we lack baseline ecological knowledge of this lemur. This dearth only serves to exacerbate their situation as conservation initiatives do not have the fundamental information needed to properly manage conservation efforts for this species. To obtain an ecological baseline for L. septentrionalis, we used instantaneous focal animal sampling to collect behavioral data, including strata use, to investigate feeding ecology for five individuals over a 12-month period (December 2018-November 2019) in Montagne des Français. We conducted a total of 755.1 hours of observation. Our results showed that L. septentrionalis’ diet consisted of mature and young leaves, ripe and unripe fruits, flo...
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently desc... more The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur
Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is... more Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations
Results of read mapping of published lemur reference genomes. Accession numbers, coverage, standa... more Results of read mapping of published lemur reference genomes. Accession numbers, coverage, standard deviation, variants and origin of tissue are listed below. (DOCX 46 kb)
Statistics from mitochondrial genomes from the five Prolemur simus and one Hapalemur griseus. Cov... more Statistics from mitochondrial genomes from the five Prolemur simus and one Hapalemur griseus. Coverage statistics as well as the GenBank Accession numbers are listed. (DOCX 61 kb)
Quality Filtering Stats from 10X genomes using Trimmomatic v0.36. (DOCX 52 kb)
Autosome Extraction Results from the KIAN8.4 MaSuRCA contigs. (DOCX 51 kb)
GenomeScope Profile of the KIAN8.4 high coverage genome. (TIFF 2484 kb)
BUSCO v2.0beta assessments of genome completeness for the five different genome assemblies, using... more BUSCO v2.0beta assessments of genome completeness for the five different genome assemblies, using the â mammalâ set of 4106 genes. (DOCX 46 kb)
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Papers by Cynthia Frasier