Dataset Information

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus).

ABSTRACT: Genealogical data are an important source of evidence for delimiting species, yet few statistical methods are available for calculating the probabilities associated with different species delimitations. Bayesian species delimitation uses reversible-jump Markov chain Monte Carlo (rjMCMC) in conjunction with a user-specified guide tree to estimate the posterior distribution for species delimitation models containing different numbers of species. We apply Bayesian species delimitation to investigate the speciation history of forest geckos (Hemidactylus fasciatus) from tropical West Africa using five nuclear loci (and mtDNA) for 51 specimens representing 10 populations. We find that species diversity in H. fasciatus is currently underestimated, and describe three new species to reflect the most conservative estimate for the number of species in this complex. We examine the impact of the guide tree, and the prior distributions on ancestral population sizes () and root age (?(0)), on the posterior probabilities for species delimitation. Mis-specification of the guide tree or the prior distribution for can result in strong support for models containing more species. We describe a new statistic for summarizing the posterior distribution of species delimitation models, called speciation probabilities, which summarize the posterior support for each speciation event on the starting guide tree.

SUBMITTER: Leache AD

PROVIDER: S-EPMC2982061 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus).

Leaché Adam D AD Fujita Matthew K MK

Proceedings. Biological sciences 20100602 1697

Genealogical data are an important source of evidence for delimiting species, yet few statistical methods are available for calculating the probabilities associated with different species delimitations. Bayesian species delimitation uses reversible-jump Markov chain Monte Carlo (rjMCMC) in conjunction with a user-specified guide tree to estimate the posterior distribution for species delimitation models containing different numbers of species. We apply Bayesian species delimitation to investigat ...[more]

PMID: 20519219

Similar Datasets

Project description:Delimitation of species is an important and controversial area within evolutionary biology. Many species boundaries have been defined using morphological data. New genetic approaches now offer more objective evaluation and assessment of the reliability of morphological variation as an indicator that speciation has occurred. We examined geographic variation in morphology of the continuously distributed skink Chalcides mionecton from Morocco and used Bayesian analyses of nuclear and mitochondrial DNA (mtDNA) loci to examine: (i) their concordance with morphological patterns, (ii) support for species delimitation, (iii) timing of speciation, and (iv) levels of gene flow between species. Four digit individuals were found at sites between Cap Rhir (in the south) and the northern extreme of the range, whereas five-digit individuals were found in two disjunct areas: (i) south of Cap Rhir and (ii) the north of the range where they were often syntopic with four-digit individuals. The pattern of variation in generalized body dimensions was largely concordant with that in digit number, suggesting two general morphotypes. Bayesian analyses of population structure showed that individuals from sites south of Cap Rhir formed one genetic cluster, but that northern four- and five-digit individuals clustered together. Statistical support for delimitation of these genetic clusters into two species was provided by a recent Bayesian method. Phylogenetic-coalescent dating with external time calibrations indicates that speciation was relatively recent, with a 95% posterior interval of 0.46-2.66 mya. This postdates equivalent phylogenetic dating estimates of sequence divergence by approximately 1 Ma. Statistical analyses of a small number of independent loci provide important insights into the history of the speciation process in C. mionecton and support delimitation of populations into two species with distributions that are spatially discordant with patterns of morphological variation.

Project description:UnlabelledForest encroachment into savanna is occurring at an unprecedented rate across tropical Africa, leading to a loss of valuable savanna habitat. One of the first stages of forest encroachment is the establishment of tree seedlings at the forest-savanna transition. This study examines the demographic bottleneck in the seedlings of five species of tropical forest pioneer trees in a forest-savanna transition zone in West Africa. Five species of tropical pioneer forest tree seedlings were planted in savanna, mixed/transition, and forest vegetation types and grown for 12 months, during which time fire occurred in the area. We examined seedling survival rates, height, and stem diameter before and after fire; and seedling biomass and starch allocation patterns after fire. Seedling survival rates were significantly affected by fire, drought, and vegetation type. Seedlings that preferentially allocated more resources to increasing root and leaf starch (starch storage helps recovery from fire) survived better in savanna environments (frequently burnt), while seedlings that allocated more resources to growth and resource-capture traits (height, the number of leaves, stem diameter, specific leaf area, specific root length, root-to-shoot ratio) survived better in mixed/transition and forest environments. Larger (taller with a greater stem diameter) seedlings survived burning better than smaller seedlings. However, larger seedlings survived better than smaller ones even in the absence of fire. Bombax buonopozense was the forest species that survived best in the savanna environment, likely as a result of increased access to light allowing greater investment in belowground starch storage capacity and therefore a greater ability to cope with fire.SynthesisForest pioneer tree species survived best through fire and drought in the savanna compared to the other two vegetation types. This was likely a result of the open-canopied savanna providing greater access to light, thereby releasing seedlings from light limitation and enabling them to make and store more starch. Fire can be used as a management tool for controlling forest encroachment into savanna as it significantly affects seedling survival. However, if rainfall increases as a result of global change factors, encroachment may be more difficult to control as seedling survival ostensibly increases when the pressure of drought is lifted. We propose B. buonopozense as an indicator species for forest encroachment into savanna in West African forest-savanna transitions.

Project description:IntroductionWildlife is an important source of protein for many people in developing countries. Yet wildlife depletion due to overexploitation is common throughout the humid tropics and its effect on protein security, especially for vulnerable households, is poorly understood. This is problematic for both sustainable rural development and conservation management.MethodsThis study investigates a key dimension of protein security in a cash-crop farming community living in a wildlife-depleted farm-forest landscape in SW Ghana, a region where protein-energy malnutrition persists. Specifically, we monitored protein sufficiency, defined as whether consumption met daily requirements, as benchmarked by recommended daily allowance (RDA). We focus on whether more vulnerable households were less likely to be able to meet their protein needs, where vulnerability was defined by wealth, agricultural season and gender of the household head. Our central hypothesis was: (a) vulnerable households are less likely to consume sufficient protein. In the context that most plant proteins were home-produced, so likely relatively accessible to all households, while most animal proteins were purchased, so likely less accessible to vulnerable households, we tested two further hypotheses: (b) vulnerable households depend more on plant protein to cover their protein needs; and (c) vulnerable households are less likely to earn sufficient cash income to meet their protein needs through purchased animal sources.ResultsBetween 14% and 60% of households (depending on plant protein content assumptions) consumed less than the RDA for protein, but neither protein consumption nor protein sufficiency co-varied with household vulnerability. Fish, livestock and food crops comprised 85% of total protein intake and strongly affected protein sufficiency. However, bushmeat remained an important protein source (15% of total consumption), especially during the post-harvest season when it averaged 26% of total protein consumption. Across the year, 89% of households experienced at least one occasion when they had insufficient income to cover their protein needs through animal protein purchases. The extent of this income shortage was highest during the lean season and among poorer households.ConclusionsThese findings indicate that despite wildlife depletion, bushmeat continues to make a substantial contribution to protein consumption, especially during the agricultural lean season. Income shortages among farmers limit their ability to purchase bushmeat or its substitutes, suggesting that wildlife depletion may cause malnutrition.

Dataset Information

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus).

Publications

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets