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5 July 2018

Community assembly and diversification in a species‐rich radiation of island weevils (Coleoptera: Cratopini) [Journal of Biogeography]

Christophe Thébaud

Aim
To test a prediction derived from island biogeographical theory that in situ speciation should make an increasingly important contribution to community assembly as islands age. This prediction is tested on estimated biogeographical histories from Mauritius (approximately 9 Myr) and Reunion (approximately 5 Myr). We additionally investigate the evolutionary dynamics of insect flight loss, as the loss of flight in island lineages can influence patterns of diversification.
Location
Mascarene Islands; Southwest Indian Ocean.
Taxon
Weevils.
Methods
Up to five individuals of each taxonomically described species sampled within each sampling site were sequenced for the mitochondrial gene Cytochrome Oxidase II to delimit operational taxonomic units (OTUs). OTUs were further sequenced for the nuclear genes Arginine Kinase, Histone 3 and ribosomal 28s, to reconstruct the phylogenetic history of the group. Timings of colonization and in situ speciation events were estimated with beast2.(...)

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5 July 2018

Multilocus phylogenetics in a widespread African anuran lineage (Brevicipitidae: Breviceps) reveals patterns of diversity reflecting geoclimatic change [Journal of Biogeography]

Keywords : climate fluctuation model, cryptic species, distribution modelling, Great Escarpment, landscape barrier model, Miocene, rain frogs

Aim
To investigate models assessing the influence of geomorphology and climatic shifts on species diversification in sub‐Saharan Africa by reconstructing the pattern and timing of phylogenetic relationships of rain frogs (Brevicipitidae: Breviceps).
Location
Sub‐Saharan Africa, south of the Congo Basin.
Methods
Multilocus sequence data were generated for near complete species‐level sampling of the genus Breviceps. Phylogenetic relationships were inferred via Bayesian inference and maximum likelihood analyses on both concatenated and single‐gene datasets. Network analyses identified locus‐specific reticulate relationships among taxa. Bayesian methods were used to infer dates of divergence among Breviceps lineages, and niche modelling was used to identify possible adaptive divergence.(...)

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5 July 2018

The value of environmental DNA biobanking for long-term biomonitoring [Nature Ecology & Evolution - Correspondence]

To the Editor — ‘Environmental DNA’ (eDNA) metabarcoding has transformed scientists’ ability to measure the diversity of multicellular life. eDNA purified from substrates such as soil or water contains DNA fragments originating from organisms present in that environment1. Determining the sequences of a select subset of these DNA fragments (‘eDNA metabarcodes’) enables taxonomic identification of the organisms from which they derive. Recent advancements in high-throughput DNA sequencing and associated technologies have improved the effectiveness of eDNA metabarcoding. This has stimulated a rapid diversification of its application to a variety of substrates and groups of target organisms (Fig. 1).

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5 July 2018

Adaptation and conservation insights from the koala genome [Nature Genetics]

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as ‘vulnerable’ due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala’s ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala’s survival in the wild.

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5 July 2018

Without quality presence–absence data, discrimination metrics such as TSS can be misleading measures of model performance [Journal of Biogeography]

Bernard Hugueny

The discriminating capacity (i.e. ability to correctly classify presences and absences) of species distribution models (SDMs) is commonly evaluated with metrics such as the area under the receiving operating characteristic curve (AUC), the Kappa statistic and the true skill statistic (TSS). AUC and Kappa have been repeatedly criticized, but TSS has fared relatively well since its introduction, mainly because it has been considered as independent of prevalence. In addition, discrimination metrics have been contested because they should be calculated on presence–absence data, but are often used on presence‐only or presence‐background data. Here, we investigate TSS and an alternative set of metrics—similarity indices, also known as F‐measures.(...)

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