Bioregion heterogeneity correlates with extensive mitochondrial DNA diversity in the Namaqua rock mouse, Micaelamys namaquensis (Rodentia: Muridae) from southern Africa - evidence for a species complex

<p>Abstract</p> <p>Background</p> <p>Intraspecific variation within the diverse southern African murine rodents has not been extensively investigated, yet cryptic diversity is evident in several taxa studied to date. The Namaqua rock mouse, <it>Micaelamys namaquensis </it>Smith, 1834 is a widespread endemic murine rodent from the subregion. Currently, a single species with four subspecies is recognised, but in the past up to 16 subspecies were described. Thus, this species is a good candidate for the investigation of patterns and processes of diversification in a diverse but under-studied mammalian subfamily and geographic region. Here, we report genetic differentiation based on mitochondrial DNA (mtDNA) cytochrome <it>b </it>(cyt <it>b</it>) sequences among samples collected over an extensive coverage of the species' range.</p> <p>Results</p> <p>Cytochrome <it>b </it>sequences of 360 widely sampled individuals identified 137 unique maternal alleles. Gene tree and phylogeographic analyses of these alleles suggest the presence of at least eight lineages or haplogroups (A-H), with varying degrees of intra-lineage diversity. This differentiation is in contrast with the most recent taxonomic treatment based on cranial morphometrics which only recognised four subspecies. The mtDNA diversity strongly supports earlier views that this taxon may represent a species complex. We further show statistical support for the association of several of these lineages with particular vegetation biomes of southern Africa. The time to the most recent common ancestor (TMRCA) dates to the Pliocene (~5 Mya) whereas coalescent-based divergence time estimates between lineages vary between 813 Kya [0.22 - 1.36] and 4.06 Mya [1.21 - 4.47]. The major diversification within lineages occurred during the Pleistocene. The identification of several regions of sympatry of distinct lineages offers future opportunities for the elucidation of the underlying speciation processes in the suggested species complex.</p> <p>Conclusions</p> <p>Similar to other African murine rodents, <it>M. namaquensis </it>radiated during the Pliocene and Pleistocene coinciding with major periods of aridification and the expansion of savanna habitats. The suggested species complex is represented by at least eight lineages of which the majority are confined to only one or a few neighbouring biomes/bioregions. Contrasting intra-lineage phylogeographic patterns suggest differences in adaptation and responses to Plio-Pleistocene climatic and vegetation changes. The role of ecological factors in driving speciation in the group needs further investigation.</p

Modelling water temperature in the lower Olifants River and the implications for climate change

Freshwater systems in southern Africa are under threat of climate change, not only from altered flow regimes as rainfall patterns change, but also from biologically significant increases in water temperature. Statistical models can predict water temperatures from air temperatures, and air temperatures may rise by up to 7 °C by 2100. Statistical water temperature models require less data input than physical models, which is particularly useful in data deficient regions. We validated a statistical water temperature model in the lower Olifants River, South Africa, and verified its spatial applicability in the upper Klaserie River. Monthly and daily temporal scale calibrations and validations were conducted. The results show that simulated water temperatures in all cases closely mimicked those of the observed data for both temporal resolutions and across sites (NSE&gt;0.75 for the Olifants River and NSE&gt;0.8 for the Klaserie). Overall, the model performed better at a monthly than a daily scale, while generally underestimating from the observed (indicated by negative percentage bias values). The statistical models can be used to predict water temperature variance using air temperature and this use can have implications for future climate projections and the effects climate change will have on aquatic species. Significance:• Statistical modelling can be used to simulate water temperature variance from observed air temperature, which has implications for future projections and climate change scenarios.• While there are many other factors affecting water temperature, air temperature accounts for up to 95% of water temperature variance.• The model used can successfully simulate water temperature variance for different rivers

Partitioning of Evaporative Water Loss into Respiratory and Cutaneous Pathways in Wahlberg's Epauletted Fruit Bats ( Epomophorus wahlbergi

Please read abstract in the article.National Research Foundation.http://www.journals.uchicago.edutoc/pbz/currenthb201

The legacy of over a century of introductions : spread debt of rainbow trout (Oncorhynchus mykiss) in Mpumalanga Province, South Africa

DATA AVAILABILITY STATEMENT : The data that support the findings of this study are openly available in WorldClim (https://worldclim.org/); Global Biodiversity Information Facility (GBIF) (https://www.gbif.org/); Protected Areas and Conservation Areas (PACA) in South Africa (https://egis.environment.gov.za/); and the South African Department of Water Affairs (https://www.dws.gov.za/iwqs/gis_data/river/All.html). In addition, species occurrence data used in the study is available as Supplementary Material. Restrictions apply to the availability of these data, which were used under license for this study.For over a century, rainbow trout (Oncorhynchus mykiss) has been widely introduced into lakes and rivers in South Africa to create and enhance sport-fishing opportunities. Despite its long history of introduction, naturalized populations of rainbow trout are still localized to a few areas with suitable habitats and climate. This study assessed the spread debt (i.e., the increase in area invaded by invasive species over time) of rainbow trout in Mpumalanga Province, South Africa to highlight areas with known introductions, the extent of the invasion, and to identify areas that are suitable for establishment but are still invasion-free. The total river length that was predicted as suitable for rainbow trout under current climate was about ca. 3,500 km in an extension of about ca. 15,000 km. Current occupancy (river length predicted as suitable with known rainbow trout occurrence records) was ca. 1,220 km (35%) and the invasion debt was therefore estimated as 65%. While these data infer a large invasion debt, they are confounded by a lack of knowledge on sampling effort and verified true absence and should therefore be recognized as an estimate. In addition, the extent of the suitable area varied under different climate change scenarios where it was projected to decrease under RCP 4.5 scenarios and increase under the RCP 8.5 scenarios. This study demonstrates some of the difficulties of quantifying the potential future extent and impacts of biological invasions and how the invasion debt concept can be applied to provide an important link between invasion biology, management, and policy.Department of Forestry, Fisheries, and the Environment, South Africa; DSI-NRF Centre of Excellence for Invasion Biology; National Research Foundation South Africa.http://wileyonlinelibrary.com/journal/rrahj2023Mammal Research InstituteZoology and Entomolog

Niche expansion by indigenous fish species following the introduction of rainbow trout (Oncorhynchus mykiss) in a subtropical river system, upper Blyde River, South Africa

SUPPLEMENTARY TABLE S1 Frequency of occurrence (%) of prey items in the diets of indigenous and alien invasive fish species in the catchments of the Blyde and Treur rivers, Mpumalanga Province, South Africa.SUPPLEMENTARY TABLE S2 Trophic position (TP), corrected Carbon (Ccorr) and values of isotopic niche (SEAc) for indigenous and alien invasive (bold) fish species sampled in uninvaded and invaded catchments of the Blyde and Treur rivers, Mpumalanga Province, South Africa.SUPPLEMENTARY TABLE S3 Isotopic niche overlap among fish species in river sections invaded by rainbow trout (Oncorhynchus mykiss) on the Blyde River, South Africa. Extent of overlap was classified as low (< 40%), intermediate (40 to 60%) and high (> 60%) (Langton, 1982).SUPPLEMENTARY TABLE S4 Isotopic niche overlap among fish species in the Treur River, South Africa that is free of rainbow trout (Oncorhynchus mykiss) invasion. Extent of overlap was classified as low (< 40%), intermediate (40 to 60%) and high (> 60%) (Langton, 1982).SUPPLEMENTARY TABLE S5 Isotopic matrices of food webs of fish communities sampled in sites invaded by rainbow trout and sites free of invasion on the Blyde and Treur rivers, Mpumalanga Province, South Africa.DATA AVAILABILITY STATEMENT : The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.The introduction of alien predatory fish such as rainbow trout (Oncorhynchus mykiss) can have a significant effect on indigenous fish communities such as altering the structure and dynamics of food webs. Quantifying the trophic niche utilised by the alien fish species is therefore important to aid our understanding of how their feeding strategies might aid establishment, define their functional role and inform on potential impacts. This study assessed food web interactions between fish communities in river reaches that are invaded by O. mykiss and sections that are free of invasions in the upper Blyde River catchment, South Africa. It specifically evaluated the hypothesis that O. mykiss invasion is likely to lead to a decrease in the trophic functional diversity through predation and that indigenous fish will shift their trophic niche to either minimise competition with, or avoid predation, by O. mykiss. Gut content and stable isotope analyses were used to determine trophic interactions. Fish communities in uninvaded areas utilised fewer and similar food sources and occupied lower trophic levels, than fish communities in invaded areas. Oncorhynchus mykiss fed mainly on invertebrates and at trophic levels similar to and or lower than indigenous fishes. This suggests that their current impact on indigenous fish communities is mainly through competition for resources. We posit that O. mykiss invasions reduced the abundance of indigenous fishes and thereby reduced predation pressure on aquatic invertebrates, with a knock-on effect on the trophic interrelationships among fish assemblages. Our findings are consistent with other studies in South Africa that have shown that the impacts of O. mykiss invasion can lead to a decline and fragmentation of indigenous species populations and niche shifts.The DSI-NRF Centre of Excellence for Invasion Biology, the South African Department of Forestry, Fisheries, and the Environment (DFFE) and the National Research Foundation.https://www.frontiersin.org/journals/environmental-scienceam2023Mammal Research InstituteZoology and Entomolog

Ecological niche modeling of the invasive potential of Nile tilapia Oreochromis niloticus in African river systems: concerns and implications for the conservation of indigenous congenerics

This study applied ecological niche models to determine the potential invasive range of Nile tilapia, Oreochromis niloticus, with a particular focus on river systems in southern Africa where it is now established and spreading. Computational tools such as niche models are useful in predicting the potential range of invasive species, but there are limitations to their application. In particular, models trained on native records may fail to predict the full extent of an invasion. This failure is often attributed to changes in either the niche of the invading species or the variables used to develop the models. In this study, we therefore evaluated the differences in the predictive power of models trained with different environmental variables, the effect of species range (native vs. introduced) on model performance and assessed whether or not there is evidence suggestive of a niche shift in Nile tilapia following its introduction. Niche models were constructed using Maxent and the degree of niche similarity was assessed using Schoener‘s index. Null models were used to test for significance. Model performance and niche conservatism varied significantly with variable selection and species range. This indicates that the environmental conditions available to Nile tilapia in its native and introduced ranges are not congruent. Nile tilapia exhibited broad invasive potential over most of southern Africa that overlaps the natural range of endemic congenerics. Of particular concern are areas which are free of exotic species but are now vulnerable due to the promotion of fish introductions mainly for aquaculture and sport fishing

Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa

Background: South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present. Results: To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven R. rattus and five R. norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with R. tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species. Conclusions: This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified

The selection of taxonomic characters for morphometric analysis: a case study based on southern African Aethomys (Mammalia: Rodentia: Muridae)

Volume: 64Start Page: 197End Page: 21

The effect of rainbow trout (Oncorhynchus mykiss) invasions on native fish communities in the subtropical Blyde River, Mpumalanga province, South Africa

This study investigated the effects of rainbow trout (Oncorhynchus mykiss) invasion on native fish communities in the upper Blyde River catchment. A fish survey was undertaken between September 2017 and October 2018 from 11 sites in the Blyde and Treur Rivers using electrofishing and fyke nets. Differences in species composition, relative abundance, and community structure among sites were tested using multivariate analysis. A total of ten fish species were captured. There were significant differences in composition and abundance between fish communities that could be attributed to O. mykiss invasion and variation in habitats. Populations of native species that historically occurred throughout the upper catchment, such as Enteromius treurensis, were greatly reduced and fragmented in the presence of O. mykiss. However, instream migration barriers such as waterfalls have prevented upstream migration of O. mykiss, and these invasion-free areas have remnant populations of native fishes that appear to be largely intact. This finding is consistent with other studies that have shown that introduced alien predatory fish can have a significant effect on fish communities and highlighted the need to prevent human-facilitated introductions in biodiversity sensitive areas, such as mountain headwater streams, that are inhabited by endemic and range-restricted minnows

Broad Niche Overlap between Invasive Nile Tilapia Oreochromis niloticus and Indigenous Congenerics in Southern Africa: Should We be Concerned?

This study developed niche models for the native ranges of Oreochromis andersonii, O. mortimeri, and O. mossambicus, and assessed how much of their range is climatically suitable for the establishment of O. niloticus, and then reviewed the conservation implications for indigenous congenerics as a result of overlap with O. niloticus based on documented congeneric interactions. The predicted potential geographical range of O. niloticus reveals a broad climatic suitability over most of southern Africa and overlaps with all the endemic congenerics. This is of major conservation concern because six of the eight river systems predicted to be suitable for O. niloticus have already been invaded and now support established populations. Oreochromis niloticus has been implicated in reducing the abundance of indigenous species through competitive exclusion and hybridisation. Despite these well-documented adverse ecological effects, O. niloticus remains one of the most widely cultured and propagated fish species in aquaculture and stock enhancements in the southern Africa sub-region. Aquaculture is perceived as a means of protein security, poverty alleviation, and economic development and, as such, any future decisions on its introduction will be based on the trade-off between socio-economic benefits and potential adverse ecological effects