The diversity of ecological interactions, both trophic and non-trophic, is central to understanding the assembly of communities. However, we have yet to study non-trophic processes through their action on ecosystem compartments such as detritus involved in both recycling and habitat provisioning. Here, we study a simple ecosystem model where the dual role of detritus as both resource and habitat allows us to define ecosystem engineering from non-trophic processes that interact with the cycling of matter at the ecosystem level. Our results show how habitat and resource limitations on consumer growth from detritus can affect ecosystem stability. We further predict that non-trophic processes can stabilize ecosystems via 1) asynchrony between trophic and non-trophic interactions, 2) weak trophic interactions emerging from non-trophic feedbacks, and 3) coupling between non-trophic and recycling processes that control top-down versus bottom-up trophic regulation. Our results show that ecosystem dynamics provide the relevant context to study the interplay between trophic and non-trophic processes.
Crunomys and Maxomys are closely related murine genera from forested regions of Southeast Asia and western portions of the Indo-Australian Archipelago. Previous phylogenetic analyses suggested that a taxonomic reappraisal is necessary for these genera, but limited taxon sampling prevented formal changes. We produced a mitochondrial DNA dataset that includes 376 individuals representing all 22 recognized species and a nuclear dataset comprising thousands of ultraconserved elements missing only 1 recognized species. Our phylogenetic inferences consistently show that Crunomys is nested within Maxomys. We transfer all Maxomys species to the older genus Crunomys to resolve the paraphyly. We also conducted a morphological analysis of species from Sulawesi and described a new species of Crunomys from the eastern peninsula of the island. We identify 43 geographically defined mitochondrial haplogroups across all species of Crunomys, many of which also are inferred as distinct in a multilocus species delimitation analysis. Historical biogeographic reconstructions consistently inferred multiple dispersal events to and from oceanic islands and among continental shelf islands and mainland Southeast Asia. On both large continental shelf islands like Borneo and large oceanic islands like Sulawesi, in situ divergence produced high levels of diversity.
Identifying and delineating species are the primary tasks of taxonomy. Owing to the decreasing interest of the nations for taxonomy and the inventory of living beings, funds have been drastically decreasing during the last two decades for taxonomic studies. As a consequence, the worldwide pool of taxonomists has dramatically decreased. DNA barcoding, as an automated tool for species delineation and identification, proved to rejuvenate the field of taxonomy and open new perspectives in ecology and conservation. In the present review, we will discuss how DNA barcoding established as a new paradigm in taxonomy and how DNA barcoding has been recently integrated in taxonomic studies. We will further detail the potential applications for species identifications and discuss how DNA barcoding may positively impact the inventory and conservation of living beings, particularly in biodiversity hotspots. We emphasise the benefit of DNA barcoding for the conservation of Southeast Asian freshwater fishes.
Southeast Asia is one of the most geologically complex tropical regions on Earth, in which the intricate interactions among plate tectonics, volcanism and Pleistocene climatic fluctuations led to complex patterns of species distribution. An increasing number of biogeographic studies of the Indonesian ichthyofauna have already partially uncovered the potential mechanisms at the origin of present day species distribution. These studies are currently scattered in the literature and the present review aims at presenting recent progress. Here, we propose a review of this literature with the aim to provide a broad overview of the current progress in the field of Indonesian freshwater fishes biogeography. First, we will briefly present the geology of the Indo-Australian Archipelago (IAA) and highlight the time frame of the geographical settlement of the Indonesian archipelago. Second, we will present the palaeoecological history of Sundaland during the Pleistocene. Finally, we will present the results of recent biogeographic studies across the three biogeographic provinces (Sundaland, Wallacea, Sahul) and discuss how these results fit with geological and palaeoecological scenarios in Indonesia.
