Ecological Restoration and Reforestation of Fragmented Forests in Kianjavato, Madagascar

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

Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data

The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar. The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We are most grateful to the Ahmanson Foundation, the Theodore F. and Claire M. Hubbard Family Foundation, the Primate Action Fund / Conservation International, the Margot Marsh Biodiversity Foundation, and the National Geographic Society, for financial assistance

Assessment of ring-tailed lemur \u3ci\u3eLemur catta\u3c/i\u3e populations in south-western Madagascar

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 65 of 83 sites in southern and south-western Madagascar, including three subpopulations that were previously considered likely to be locally extinct. We identified a minimum of 792 L. catta individuals (summing only maximum group sizes at each site) and as many as 1,221 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

Dietary flexibility of the greater bamboo lemur (Prolemur simus), a specialized feeder, in eastern Madagascar

The degree of dietary flexibility in primates is species specific; some incorporate a wider array of resources than others. Extreme interannual weather variability in Madagascar results in seasonal resource scarcity which has been linked to specialized behaviors in lemurs. Prolemur simus, for example, has been considered an obligate specialist on large culm bamboo with >60% of its diet composed of woody bamboos requiring morphological and physiological adaptations to process. Recent studies reported an ever‐expanding list of dietary items, suggesting that this species may not be an obligate specialist. However, long‐term quantitative feeding data are unavailable across this species’ range. To explore the dietary flexibility of P. simus, we collected data at two northern sites, Ambalafary and Sahavola, and one southern site, Vatovavy, from September 2010 to January 2016 and May 2017 to September 2018, respectively. In total, we recorded 4022 h of behavioral data using instantaneous sampling of adult males and females from one group in Ambalafary, and two groups each in Sahavola and Vatovavy. We recorded 45 plant species eaten by P. simus over 7 years. We also observed significant differences in seasonal dietary composition between study sites. In Ambalafary, bamboo was the most frequently observed resource consumed (92.2%); however, non‐bamboo resources comprised nearly one‐third of the diet of P. simus in Sahavola and over 60% in Vatovavy. Consumption of all bamboo resources increased during the dry season at Ambalafary and during the wet season at Vatovavy, but never exceeded non‐bamboo feeding at the latter. Culm pith feeding was only observed at Ambalafary, where it was more common during the dry season. We identify P. simus as a bamboo facultative specialist capable of adjusting its feeding behavior to its environment, indicating greater dietary flexibility than previously documented, which may enable the species to survive in increasingly degraded habitats

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Evolution and systematics of the angiosperm order Gentianales with an in-depth focus on Loganiaceae and its species-rich and toxic genus Strychnos

The Gentianales includes five families known for their horticultural value and medicinal effects: Apocynaceae (milkweeds and rosy periwinkle), Gelsemiaceae (Carolina jessamine), Gentianaceae (gentians), Loganiaceae (strychnine plants), and Rubiaceae (coffee and quinine). They are a monophyletic assemblage, but the relationships between the families have been uncertain. The Loganiaceae are a mostly pantropical group with a few members reaching into temperate North America and Australia. This family includes 15 genera that have been divided into four tribes, one of which, Strychneae, was paraphyletic in previous analyses based on chloroplast and morphological data. Strychnos is the largest genus in Loganiaceae with approximately 200 species distributed throughout the tropics. This genus is well-known for its alkaloid production, in particular that of strychnine. Although strychnine has been popularized for its potential nefarious uses, many Strychnos species have been lauded for their medicinal properties conferred by other compounds. Strychnos was divided into 12 sections based on morphology, but the monophyly of these was in doubt as the sections were morphologically, chemically, and anatomically heterogenous. Combined analyses of four chloroplast regions, matK, ndhF, rbcL, and trnL, placed Rubiaceae as the most basal family in the Loganiaceae. Loganiaceae and Gelsemiaceae were the two subsequently diverging clades, and Apocynaceae and Gentianaceae were sisters in the most nested position. Within the Loganiaceae, tribe Antonieae was basal to all other tribes. Strychneae was resolved as monophyletic only when morphology was included in a combined analysis with a nuclear ribosomal gene region (ITS) and rps16 of the chloroplast genome. An analysis of the secondary structure of the ITS region resulted in possible new synapomorphies for tribes Antonieae and Spigelieae within the Loganiaceae. The current sectional treatment of Strychnos does not reflect the evolution of the genus, and recommendations for improving the classification will be made. This work will have large implications for the understanding of chemical and morphological evolution on ordinal, familial, and tribal levels in the Gentianales, and provides a framework for further studies in biogeography, habit evolution, and speciation processes.Ph.D.Includes bibliographical references

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

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

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

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

lepitotalm23nhmpannotationtreefromBeast

The Bayesian tree with divergence time from lepitotalm23Beast.xml by BEAST packag

Data from: Phylogenomic reconstruction of sportive lemurs (genus Lepilemur) recovered from mitogenomes with inferences for Madagascar biogeography

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