Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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Modern Applied Statistics With S

I. the origin of species by means of natural selection

Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status.

/pdf/global-effects-of-land-use-on-local-terrestrial-biodiversity-31yzxze5ly.pdf

Global effects of land use on local terrestrial biodiversity

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

Ten years of research on Bolivian amphibians: updated checklist, distribution, taxonomic problems, literature and iconography

http://justinyeager.org/papers/SmellOfSuccess.pdf

The smell of success: choice of larval rearing sites by means of chemical cues in a Peruvian poison frog

The use of species distribution models (SDMs) to predict potential distributions of species is steadily increasing. A necessary assumption when projecting models throughout space or time is that climatic niches are conservative, but recent findings of niche shifts during biological invasion of particular plant and animal species have indicated that this assumption is not categorically valid. One reason for observed shifts may relate to variable selection for modelling. In this study, we assess differences in climatic niches in the native and invasive ranges of the Greenhouse frog (Eleutherodactylus planirostris). We analyze which variables are more ‘conserved’ in comparison to more ‘relaxed’ variables (i.e. subject to niche shift) and how they influence transferability of SDMs developed with Maxent on the basis of ten bioclimatic layers best describing the climatic requirements of the target species. We focus on degrees of niche similarity and conservatism using Schoener's index and Hellinger distance. Significance of results are tested with null models. Results indicate that the degrees of niche similarity and conservatism vary greatly among the predictive variables. Some shifts can be attributed to active habitat selection, whereas others apparently reflect variation in the availability of climate conditions or biotic interactions between the frogs' native and invasive ranges. Patterns suggesting active habitat selection also vary among variables. Our findings evoke considerable implications on the transferability of SDMs over space and time, which is strongly affected by the choice and number of predictors. The incorporation of ‘relaxed’ predictors not or only indirectly correlated with biologically meaningful predictors may lead to erroneous predictions when projecting SDMs. We recommend thorough assessments of invasive species' ecology for the identification biologically meaningful predictors facilitating transferability.

Explanative power of variables used in species distribution modelling: an issue of general model transferability or niche shift in the invasive Greenhouse frog (Eleutherodactylus planirostris).

Anthropogenic climate change poses a major threat to global biodiversity with a poten-tial to alter biological interactions at all spatial scales. Amphibians are the most threatened verte-brates and have been subject to increasing conservation attention over the past decade. A particularconcern is the pandemic emergence of the parasitic chytrid fungus Batrachochytrium dendrobatidis ,which has been identified as the cause of extremely rapid large-scale declines and species extinc-tions. Experimental and observational studies have demonstrated that the host–pathogen system isstrongly influenced by climatic parameters and thereby potentially affected by climate change.Herein we project a species distribution model of the pathogen onto future climatic scenarios gener-ated by the IPCC to examine their potential implications on the pandemic. Results suggest that pre-dicted anthropogenic climate change may reduce the geographic range of B. dendrobatidis and itspotential influence on amphibian biodiversity.KEY WORDS: Amphibia · Anthropogenic future climate change ·

/pdf/future-potential-distribution-of-the-emerging-amphibian-1e1v03zmgz.pdf

Future potential distribution of the emerging amphibian chytrid fungus under anthropogenic climate change.

Amphibians at the global scale are dramatically declining and the pathogenic fungus Batrachochytrium dendrobatidis (Bd) has been suggested to be an important driver in this biodiversity crisis. Increasing evidence points towards the global emergence of Bd being a panzootic caused by pathogen pollution. Africa has been suggested to be the origin of the pathogen but remains one of the least-studied areas. We have conducted the most comprehensive survey on the continent to date focusing on Kenya for investigating taxonomic and environmental components in the distribution of Bd in tropical Africa. Eleven sites along a 770 km transect from the coast up to the border of Uganda were surveyed. Using quantitative PCR, we screened 861 samples from 23 different species in nine genera. The pathogen was confirmed at all studied sites, with an overall prevalence of 31.5%. No dead or symptomatic specimens were found and no declines have been reported in the region so far. Both prevalence and parasite load ranged from the detection limit to some of the highest ever reported. The parasite load showed a significant taxonomic bias and a strong inverse correlation with temperature. Our findings suggest that Bd may be enzootic in the region. We recommend that further research should focus on comparative experimental studies of susceptibility to Bd in African species. Moreover, we stress the need for improved knowledge on the conservation status of the tropical African amphibian fauna to confirm the enzootic nature of widespread Bd infections.

https://zslpublications.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-1795.2009.00297.x

Stefan Lötters

Papers

Ten years of research on Bolivian amphibians: updated checklist, distribution, taxonomic problems, literature and iconography

The smell of success: choice of larval rearing sites by means of chemical cues in a Peruvian poison frog

Explanative power of variables used in species distribution modelling: an issue of general model transferability or niche shift in the invasive Greenhouse frog (Eleutherodactylus planirostris).

Future potential distribution of the emerging amphibian chytrid fungus under anthropogenic climate change.

Widespread occurrence of the amphibian chytrid fungus in Kenya