Next-generation mitogenomics: A comparison of approaches applied to caecilian amphibian phylogeny

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case

Local extinctions of insular avifauna on the most remote inhabited island in the world

Published OAThe overwhelming majority of avian extinctions have occurred on islands, where introduced predators, habitat loss, disease, and human persecution have resulted in the loss of over 160 species in the last 500 years. Understanding the timing and causes of these historical extinctions can be beneficial to identifying and preventing contemporary biodiversity loss, as well as understanding the nature of island ecosystems. Tristan da Cunha (henceforth “Tristan”), the most remote inhabited island in the world, has lost three species from the main island since permanent human settlement in 1811—the Tristan Moorhen (Gallinula nesiotis), Inaccessible Finch (Nesospiza acunhae acunhae), and Tristan Albatross (Diomedea dabbenena). We used recently developed Bayesian methods, and sightings of mixed certainty compiled from historical documents, to estimate the extinction date of these three species from Tristan based on specimens. We estimate that all three species were likely extirpated from Tristan between 1869 and 1880 following a period of significant habitat alteration and human overexploitation, and only the albatross had a high probability of persistence when Black Rats (Rattus rattus) arrived in 1882, the previously assumed cause of extinction for all three species. Better estimates of extinction dates are essential for understanding the causes of historical biodiversity loss, and the combination of historical ecology with modern statistical methods has given us novel insights into the timing and therefore the causes of extinctions on one of the most isolated islands in the world.© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The attached file is the published version of the article