Zhu, Di Wu, Feng Li, Hailong Wang, Tianming Bao, Lei Ge, Jianping Wang, Hongfang
Published in
Molecular ecology resources
High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator-prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In th...
LeBlanc, Nathalie M Pavey, Scott A
Published in
Molecular ecology resources
In this study, we used the phenotype simulation package naturalgwas to test the performance of Zhao's Random Forest method in comparison to an uncorrected Random Forest test, latent factor mixed models (LFMM), genome-wide efficient mixed models (GEMMA), and confounder adjusted linear regression (CATE). We created 400 sets of phenotypes, correspondi...
Hua, Zhongyi Jiang, Chao Song, Shuhui Tian, Dongmei Chen, Ziyuan Jin, Yan Zhao, Yuyang Zhou, Junhui Zhang, Zhang Huang, Luqi
...
Published in
Molecular ecology resources
Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-m...
Walton, Kerry Scarsbrook, Lachie Mitchell, Kieren J Verry, Alexander J F Marshall, Bruce A Rawlence, Nicolas J Spencer, Hamish G
Published in
Molecular ecology resources
Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Her...
Yang, Shangchen Lan, Tianming Zhang, Yi Wang, Qing Li, Haimeng Dussex, Nicolas Sahu, Sunil Kumar Shi, Minhui Hu, Mengyuan Zhu, Yixin
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Published in
Molecular ecology resources
Critically endangered species are usually restricted to small and isolated populations. High inbreeding without gene flow among populations further aggravates their threatened condition and reduces the likelihood of their long-term survival. Chinese alligator (Alligator sinensis) is one of the most endangered crocodiles in the world and has experie...
Jeunen, Gert-Jan Dowle, Eddy Edgecombe, Jonika von Ammon, Ulla Gemmell, Neil J Cross, Hugh
Published in
Molecular ecology resources
The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomical...
Tello, Daniel Gonzalez-Garcia, Laura Natalia Gomez, Jorge Zuluaga-Monares, Juan Camilo Garcia, Rogelio Angel, Ricardo Mahecha, Daniel Duarte, Erick Leon, Maria Del Rosario Reyes, Fernando
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Published in
Molecular ecology resources
Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we pr...
Samuk, Kieran
Published in
Molecular ecology resources
Konopiński (2022) suggests that when averaging nucleotide diversity over a sequence, ignoring per-site sample size variation (i.e., using an unweighted mean) offers an improvement in precision (lower variation) and accuracy (reduced bias). Here, I argue that preserving uncertainty due to variation in sample size is in line with best statistical pra...
Dopheide, Andrew Brav-Cubitt, Talia Podolyan, Anastasija Leschen, Richard A B Ward, Darren Buckley, Thomas R Dhami, Manpreet K
Published in
Molecular ecology resources
Despite recent advances in high-throughput DNA sequencing technologies, a lack of locally relevant DNA reference databases limits the potential for DNA-based monitoring of biodiversity for conservation and biosecurity applications. Museums and national collections represent a compelling source of authoritatively identified genetic material for DNA ...
Li, Tian-Chu Miao, Yun-Heng Wang, Tao Zu, Guo-Hao Huang, Da-Wei Xiao, Jin-Hua
Published in
Molecular ecology resources
DNA barcoding and metabarcoding have been increasingly used in species delimitation and species diversity assessment, respectively, and the molecular markers used in animals are mainly derived from mitochondrial DNA. It is well known that the phenomenon of multiple mitochondrial haplotypes within the same specimen (hereafter referred to as "mitotyp...
