Biology subjects

James, S. W.

Publications and source records attributed to James, S. W..

3 recordsLinked to original sources

bioRxiv2024

The applicability of Regional Red List assessments for soil invertebrates: First assessment of five native earthworm species in Canada

Earthworms (Annelida: Clitellata: Crassiclitellata) are prominent members of the soil community, important to many ecosystem functions. Despite this, and like many other soil invertebrates, they are rarely considered in conservation assessments, including the IUCN Red List assessments used to assess species extinction risk. To investigate the applicability of the IUCN Regional Red Listing protocol to soil invertebrates, we assessed the conservation status of five earthworm species known to be native to Canada using this protocol and all available occurrence records. In Canada, no earthworm species have yet been assessed by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). Due to the lack of data on population sizes and their trends, all five species were assessed using their Extent of Occurrence (EOO) (Criterion B). One species was assessed as Vulnerable, two were assessed in non-threatened categories, and two were assessed as Data Deficient. For the majority, the main threats identified were the continuing loss of potential habitat due to land conversion and resource exploitation, as well as the effects of climate change. Increasing the amount of data, including but not limited to distribution and habitat preferences, would make the assessment process easier and status decisions better supported. By undertaking regional assessments for five native earthworm species in Canada, we show that Regional Red List assessments are feasible for soil invertebrates.

ecology↗

bioRxiv2019

Molecular mechanisms behind global distribution of earthworm revealed by the genome

Earthworms (Annelida: Crassiclitellata), are widely distributed around the world due to their great adaptability. However, lack of a high-quality genome sequence prevents gaining the many insights into physiology, phylogeny, and genome evolution that could come from a good earthworm genome. Herein, we report a complete genome assembly of the earthworm Amynthas corticis of about 1.2 Gb, based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the earthworm genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows 97 immune related proteins and 16S rDNA sequences shows 88 microbes with significantly response to pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, may explain its powerful defensive functions adapt to complex environment and invasion from molecular level.

genomics↗

bioRxiv2019

Anthropogenic Soils Promote Biodiversity in Amazonian Rainforests

Amazonian Dark Earths (ADEs) are fertile anthropic soils found throughout Amazonia, resulting from long-term occupation by pre-Columbian societies. Although the chemistry of these soils is well known, their biodiversity, particularly soil invertebrate communities have been neglected. To address this, we characterised soil macroinvertebrate communities and their activities in ADEs, comparing them with adjacent reference soils under forests and agriculture, at nine archaeological sites. We found 667 morphospecies and a tenacious pre-Columbian biodiversity footprint, with 40% of species found exclusively in ADEs. Soil biological activity was higher in ADEs than in adjacent soils, and associated with higher biomass and richness of organisms known to engineer the ecosystem. We show that these habitats have unique species pools, but that contemporary land-use causes nutrient loss and threatens their diversity. Both past and present human activities alter biodiversity and its distribution in Amazonia, and further efforts are needed to recognize and preserve these ADEs and their biodiversity.

zoology↗