1 Gravel beaches in the Mediterranean ecoregion represent an economically important and unique habitat type. Yet, burgeoning tourism, intensive coastal development and artificial nourishment of beaches may jeopardize their ecological communities. To date, species that reside on gravel beaches and the consequences of beach alterations are poorly understood, which hampers the development of a sustainable coastal tourism industry along the region’s shorelines. 2 Using a simple collection method based on dredging buckets through the intertidal section of beaches, we quantified the microhabitat association of two sympatric clingfish species in the genus Gouania at seven natural and an artificial gravel beach based on sediment characteristics. We hypothesized that slender (G. pigra) and stout (G. adriatica) morphotypes would partition interstitial niche space based on sediment size, which may affect the vulnerability of the species to changes in gravel beach composition due to coastal development. 3 We detected substantial differences in gravel composition within and among the sampled beaches which suggests scope for microhabitat partitioning in Gouania. Indeed, we found significant relationships between species identity and the presence/absence and abundance of individuals in hauls based on their positioning on PC1. 4 Our results suggest that modifications of gravel beaches through coastal development, including beach nourishment, intensifying coastal erosion, or artificial beach creation, may have detrimental consequences for the two species if sediment types or sizes are altered. We posit that, given the simplicity and efficacy of our sampling method and the sensitivity of Gouania species to prevailing gravel composition, the genus could serve as an important indicator for gravel beach management in the Mediterranean ecoregion.
Maternal lineages of mitochondrial DNA (mtDNA) are recognized as important components of intra- and inter-specific biodiversity and help us to disclose the phylogeny and divergence times of many taxa. Species of the genus Capra are canonical mountain dwellers. Among these is the Siberian ibex (Capra sibirica), which is regarded as a relic species whose intra-specific classification has been controversial so far. We collected 54 samples in Xinjiang, China, and analyzed the mtDNA genes to shed light on the intra-specific relationships of the C. sibirica populations and estimate the divergence time. Intriguingly, we found that the mtDNA sequences of C. sibirica split into two main lineages in both phylogenetic and network analyses: the southern lineage, sister to C. falconeri, consisting of samples from India, Ulugqat, and Kagilik in Xinjiang; and the northern lineage further divided into four monophyletic clades A–D corresponding to their geographic origins. Samples from Urumqi, Sawan, and Arturk formed a distinct monophyletic clade C within the northern lineage. The genetic distance between the C. sibirica clades ranges from 3 to 8.6 percent, with values of FST between 0.72 and 0.95, indicating notable genetic differentiation. The split of the genus Capra occurred approximately 6.75 Mya during the late Miocene. The northern lineage diverged around 5.88 Mya, following the divergence of Clades A–D from 3.3 Mya to 1.9 Mya during the late Pliocene and early Pleistocene. The radiation between the southern lineage and C. falconeri occurred at 2.29 Mya during the early Pleistocene. Our results highlight the importance of extensive sampling when relating to genetic studies of alpine mammals and call for further genomic studies to draw definitive conclusions.
The complete mitochondrial genomes of two Prophantis species in the tribe Trichaeini (Lepidoptera: Crambidae) were sequenced using high-throughput sequencing technology. They were assembled and annotated: the complete mitogenomes of P. octoguttalis and P. adusta were 15,197 bp and 15,714 bp, respectively, and contain 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. Their arrangement was consistent with the first sequenced mitogenome of Lepidoptera, from Bombyx mori (Bombycidae). The nucleotide composition was obviously AT-biased, and all protein-coding genes, except for the cox1 gene (CGA), used ATN as the start codon. Except for trnS1, which lacked the DHU arm, all tRNA genes could fold into the clover-leaf structure. Phylogenetic trees of Crambidae were reconstructed based on mitogenomic data using Maximum likelihood (ML) and Bayesian inference (BI) analysis methods. Results showed that Trichaeini in this study robustly constitute a monophyletic group in Spilomelinae, with the relationships (Trichaeini + Nomophilini) + ((Spilomelini + (Hymeniini + Agroterini)) + Margaroniini). However, the affinities of the six subfamilies Acentropinae, Crambinae, Glaphyriinae, Odontiinae, Schoenobiinae and Scopariinae within the “non-PS Clade” in Crambidae remained doubtful with unstable topologies or low supports.
Body condition is a frequently used physiological indicator of avian health and is affected by an array of environmental variables. Although a number of studies have investigated the specific effects of individual weather variables on body condition in birds, few have analyzed the effects of both temperature and precipitation within the context of an extreme weather event such as hurricanes. In this study we examined the relationship between breeding season body condition and daily maximum temperature, daily minimum temperature, and monthly total precipitation for three passerine bird species at the Welder Wildlife Refuge near Rockport, Texas. We also evaluated yearly changes in body condition over a twelve-year period for northern cardinals (Cardinalis cardinalis), painted buntings (Passerina ciris), and white-eyed vireos (Vireo griseus), focusing on the extreme precipitation event of Hurricane Harvey which caused heavy localized flooding. We found that body condition declined with average daily minimum and maximum temperatures, while precipitation had varied, species-specific effects in the three species analyzed. Our results also suggest that northern cardinals experienced a notable reduction in average body condition in the two years following Hurricane Harvey. Taken together, we conclude that short-term precipitation and temperature drivers can be important correlates of body condition in songbirds and that severe weather events may reduce body condition in some bird species.
Raptors are apex predators threatened globally by electrocution, collisions, and habitat fragmentation. Most species of raptors are understudied and largely unexplored. Top predators like raptors depend on the sustainability of the ecosystems in which they live and migrate. Knowing how endangered raptors are geographically dispersed, as well as the factors that may influence how they use their habitat, is critical for their protection. This research focuses on Kenya, where there are gaps in knowledge on appropriate habitats and raptor dispersal patterns. With several species of raptors endangered, it is crucial to determine their distribution patterns for management and conservation. To evaluate the size of the realized niches for five Kenyan raptor species at the risk of extinction, we applied species distribution models (SDMs) through an ensembling approach using occurrence data from the Global Biodiversity Information Facility (GBIF) and environmental covariates. These species were: Martial eagle, Secretarybird, Bateleur, Steppe Eagle, and Southern ground hornbill. The five raptors’ distribution within and outside protected areas and the role of key environmental predictors in predicting their distribution was estimated. Our findings indicate raptor distribution in several areas in Kenya that is predominantly in the south-western region, extending into the country’s central region. Martial eagle had the largest niche range amounting to ca.49,169 km2 while the Southern ground hornbill had the smallest niche range amounting to ca.4,145 km2. Secretarybird had the highest distribution outside protected areas at 77.57% followed by the Martial eagle at 76.89%. Significant predictors of raptor species distribution in Kenya were; precipitation during the warmest quarter, precipitation during the driest month, and precipitation during the coldest quarter. Key areas for raptor conservation listed here could serve as foundation for a number of additional Important Bird Areas (IBAs) in Kenya, according to the A1 Global IBA Criterion for species that are globally threatened.
Inter-specific adoption is an intriguing topic in behavioural and evolutionary ecology. Being a rare phenomenon is rarely documented in the literature and thus reports of inter-specific adoption based on solid data are particularly valuable. Here, owing to a long-term and extensive monitoring of a local population of the European blackbird (Turdus merula, hereafter blackbird), we describe observations of alloparental behaviour exhibited by blackbirds towards fieldfare (Turdus pilaris) nestlings (single nest, first record ever) and fledglings (twelve cases in total). We discuss the observations in respect to available literature.
Reliable estimates of population size and demographic rates are central to assessing the status of threatened species. However, obtaining individual-based demographic rates requires long-term data, which is often costly and difficult to collect. Photographic data offer an inexpensive, non-invasive method for individual-based monitoring of species with unique markings, and could therefore increase available demographic data for many species. However, selecting suitable images and identifying individuals from photographic catalogues is prohibitively time-consuming. Automated identification software can significantly speed up this process. Nevertheless, automated methods for selecting suitable images are lacking, as are studies comparing the performance of the most prominent identification software packages. In this study, we develop a framework that automatically selects images suitable for individual identification, and compare the performance of three commonly used identification software packages; Hotspotter, I3S-Pattern, and WildID. As a case study, we consider the African wild dog Lycaon pictus, a species whose conservation is limited by a lack of cost-effective large-scale monitoring. To evaluate intra-specific variation in the performance of software packages, we compare identification accuracy between two populations (in Kenya and Zimbabwe) that have markedly different coat colouration patterns. The process of selecting suitable images was automated using Convolutional Neural Nets that crop individuals from images, filter out unsuitable images, separate left and right flanks, and remove image backgrounds. Hotspotter had the highest image-matching accuracy for both populations. However, the accuracy was significantly lower for the Kenyan population (62%), compared to the Zimbabwean population (88%). Our automated image pre-processing has immediate application for expanding monitoring based on image-matching. However, the difference in accuracy between populations highlights that population-specific detection rates are likely and may influence certainty in derived statistics. For species such as the African wild dog, where monitoring is both challenging and expensive, automated individual recognition could greatly expand and expedite conservation efforts.
Habitat loss and habitat fragmentation usually occur together, at the same time and place. However, while there is consensus that habitat loss is the preeminent threat to biodiversity, the effects of fragmentation are contentious. Some argue that habitat fragmentation is not bad for biodiversity, and even that it is good. Generally, the studies that find no harm or positive outcomes of fragmentation invariably assume that it is independent of habitat loss. However, dissociating the effects of habitat fragmentation from habitat loss is questionable because of the two are essentially coupled. Accordingly, we evaluated how forest area and fragmentation (via edge effects) influenced dung beetles per se, and through their effects on the abundance of mammals, using structural equation modeling (SEM). Dung beetles are very sensitive to forest habitat loss and fragmentation, and to changes in the abundance of mammals on which they depend for dung. Our study area was in the Tana River, Kenya, where forest fragments are depauperate of mammals except for two endemic species of monkeys. We mapped 12 forests, counted the resident monkeys, and sampled 113,959 beetles from 288 plots. Most of the 87 species of beetles were small, affirming the endemic monkeys as the main source of dung. After implementing a fully latent Structural Regression SEM, the optimal model explained a significant 26% of the variance in abundance, and 89% of diversity. The main drivers of beetle abundance were positive, direct, effects of forest area and number of monkeys, and negative edge effects. The main drivers of diversity were the direct effects of the beetle abundance, indirect effects of forest area and abundance of mammals, and indirect negative edge effects. Thus forest area, fragmentation (via edge effects) and the number of monkeys jointly influenced the abundance and diversity of the beetles directly and indirectly.
Aim: The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species. It is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations, but also poses a potential disease risk to other species, including humans and livestock. Despite the imminent threat to the species’ survival and its prevalence in the wildlife trade, the phylogeography and evolution of the Sunda pangolin is not well understood. We aimed to investigate the species’ phylogeography across its distribution to improve our understanding of the species’ evolutionary history, elucidate any taxonomic uncertainties and enhance the species’ conservation genetic management and wildlife forensics applications. Location: Southeast Asia and southern China. Methods: We sequenced mtDNA genomes from 23 wild Sunda pangolins from Borneo and Peninsular Malaysia. We used these data in conjunction with previous generated mtDNA and nuclear datasets from across the species’ range to perform various phylogenetic and population genetic analyses. Results: We identified an evolutionarily distinct mtDNA lineage in north Borneo, which was estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time of the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. Main conclusions: These findings are consistent with the ‘out of Borneo hypothesis’, whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex, and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic species identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.
Practical lab skills are rarely directly assessed. To improve constructive alignment between described learning outcomes of practical skills and assessment, we developed and tested a certification procedure for microscopy skills. The procedure was embedded into the ordinary learning activity, so no additional time was needed. Three slightly different protocols were developed within the framework of sociocultural learning theory and built like a skill ladder including direct peer assessment and elements of gamified learning. The protocols varied slightly in the way students were prepared for the certification, the number of steps/levels of achievement, and the consequences of failing. We tested the protocols at three different academic institutions and within 11 courses of varying sizes and academic levels in biology or geology. Feedback were collected through online surveys (n = 207) or orally after sessions. One protocol provided instruction videos as preparation material. Instruction videos provided increased understanding of the task, but tactile training was most important for learning. Regardless of institution, type of preparation, and level of former experience, the certification procedure made students clearly more engaged in the exercise. The majority reported that the certification procedure increased their motivation to learn, increased their learning outcome, and was appropriate for assessing practical skills. Students with no or little experience in microscopy before the exercise were more positive about the certification procedure compared to skilled students, and the level of engagement and preparation was higher when there were some consequences of failing. Most students felt comfortable being certified by peers, but some students expressed concern about peers making mistakes. The presented certification procedure can easily be adapted to assess other practical skills, and with some adjustments be an efficient method for assessment-as-learning, merging formative- and summative assessment.
Rapid economic development can pose a threat to the biodiversity of tropical countries. In Laos, this is manifested by the conversion of natural forests into plantations, even though this area is one of the biodiversity hotspots of Southeast Asia. Beetle communities can be good indicators of the impact of anthropogenic pressure on natural ecosystems. In this study, we analyzed for the first time a countrywide inventory of Coleoptera to assess the ecological and anthropogenic drivers of beetle communities in Laos. We examined beetle communities (described at the family level) across the country, located in distinct habitat types, in order to understand the impact a rapid increase in human activities has on the region’s biodiversity. We found that beetle abundance had declined in plantations compared to natural forests. At the same time, we observed fewer beetle families in plantations overall, but at the scale of sampling sites there was no difference in local diversity compared to natural forests, suggesting a homogenization of beetle communities in anthropogenic habitats. Although results are certainly sensitive to our coarse classification of beetle specimens into families, the negative impact of the conversion of natural tropical forests into agriculture area can still be clearly demonstrated. Our findings highlight that it is possible to make use of unstructured large-scale inventories to explore how beetle communities responds to landscape changes induced by human activities. We suggest that sampling beetle communities can be used as an ecological indicator to monitor anthropogenic impacts on tropical ecosystems.
Species boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species-level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb-I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY), and cytb genetic distances values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex.
Many reef invertebrates reproduce through simultaneous broadcast spawning, with an apparent advantage of overwhelming potential predators and maximizing propagule survival. Although reef fish have been observed to consume coral gamete bundles during spawning events, there are no published records of such predation by benthic invertebrates. Here, we document several instances of the ruby brittle star, Ophioderma rubicundum, capturing and consuming egg-sperm bundles of the mountainous star coral, Orbicella faveolata, and the symmetrical brain coral, Pseudodiploria strigosa, during spawning events in the Cayman Islands in 2012 and the Florida Keys in 2022. These observations are widely separated in space and time (>600 km, 10 years), suggesting that this behavior may be ubiquitous on western Atlantic reefs. Since O. rubicundum spawns on the same or subsequent nights as these coral species, we hypothesize that this opportunistic feeding behavior takes advantage of the coral’s lipid-rich bundles to recover energy reserves expended by the brittle star during gametogenesis. The consumption of coral gametes by adult brittle stars suggests a novel trophic link between reef invertebrates, and also provides evidence that ophiuroid-coral symbioses may oscillate between commensalism and parasitism depending on the ontogeny and reproductive status of both animals. Our observations provide insights into the nuanced, dynamic associations between coral reef invertebrates and may have implications for coral fecundity and resilience.
Avian diet can be affected by site-specific variables, such as habitat, as well as intrinsic factors such as sex. This can lead to dietary niche separation, which reduces competition between individuals, as well as impacting how well avian species can adapt to environmental variation. Estimating dietary niche separation is challenging, due largely to difficulties in accurately identifying food taxa consumed. Consequently, there is limited knowledge of the diets of woodland bird species, many of which are undergoing serious population declines. Here, we show the effectiveness of multi-marker faecal metabarcoding to provide in-depth dietary analysis of a declining passerine, the Hawfinch (Coccothraustes coccothraustes). We collected faecal samples from (n=262) UK Hawfinches prior to, and during the breeding seasons in 2016-2019. We detected 49 and 90 plant and invertebrate taxa, respectively. We found Hawfinch diet varied spatially, as well as between sexes, indicating broad dietary plasticity and the ability of Hawfinches to utilise multiple resources within their foraging environments.
To predict suitable growing regions for Leonurus japonicus and to provide scientific sopport for the habitat conservation and the exploitation and utilization of germplasm resources under climate change conditions, this study combined niche and priority conservation models to assess the future potential distribution of L. japonicus in China. To this end, distribution points and samples of L. japonicus were gathered through online and field surveys. The Maxent model with optimized parameters was used for predicting the suitable habitats of L. japonicus at different stages, and the Marxan model was used to determine the priority of protected areas. The results showed that the highest temperature in the hottest month, the lowest temperature in the coldest month, the precipitation in the wettest month, the precipitation in the driest month, and altitude were the main environmental factors influencing the distribution of L. japonicus. Under the three climate change scenarios, the centroid of the suitable area of L. japonicus migrated northward, and the migration position tended to expand further northwest. In the future, there would be no significant niche differentiation of L. japonicus; the Marxan results showed that priority protected areas for L. japonicus were in southwestern central China, Lingnan, southern east China, and Guizhou. Overall, the results of this research can provide a strategy for the determination of priority protection areas for Leonurus japonicus in China.
The interaction of recent orographic uplift and climate heterogeneity acted as a key role in the East Himalaya-Hengduan Mountains (EHHM) has been reported in many studies. However, how exactly the interaction promotes clade diversification remains poorly understood. Here, we both studied genetic structure of the chloroplast trnT-trnF region and 11 nuclear microsatellite loci in Hippophae gyantsensis and examined what role geological barriers or ecological factors play in the spatial genetic structure. The results showed that this species had a strong east-west phylogeographic structure, with several mixed populations identified from microsatellite data in central location. The intraspecies divergence time was estimated to about 3.59 Ma, corresponding well with the recent uplift of the Tibetan Plateau. Between the two lineages there was significant climatic differentiation without geographic barriers. High consistency between lineage divergence, climatic heterogeneity and Qingzang Movement demonstrated that climatic heterogeneity but not geographic isolation drives the divergence of H. gyantsensis, and the recent regional uplift of the QTP, as the Himalayas, create heterogeneous climates by affecting the flow of the Indian monsoon. The east group of H. gyantsensis experienced population expansion c. 0.12 Ma, closely associated with the last interglacial interval. Subsequently, a genetic admixture event between east and west groups happened at 26.90 ka, a period corresponding to the warm inter-glaciation again. These findings highlight the importance of the Quaternary climatic fluctuations in the recent evolutionary history of H. gyantsensis. Our study will improve the understanding of the history and mechanisms of biodiversity accumulation in the EHHM region.
Seasonal dietary shifts of animals are important ecological adaptation strategies. An increasing number of studies have shown that seasonal dietary shifts can influence or even determine the composition of gut microbiota. The turpan wonder gecko Teratoscincus roborowskii lives in extreme desert environments, which have flexible dietary shift to fruit-eating in warm seasons. But the impact of such shifts on gut microbiota is poorly understood. Here, 16SrRNA sequencing and LC-MS metabolomics we used to examine the changes of gut microbiota composition and metabolic pattern of T. roborowskii. The results demonstrated that the gut microbes of T. roborowskii had significant seasonal changes, the diversity and abundance of gut microbiota in autumn were higher than those of in spring. Firmicutes, Bacteroidetes and Proteobacteria were the core gut microbes of T. roborowskii. Verrucomicrobia and Proteobacteria exhibit dynamic pattern of ebb and flow between spring and autumn.The composition and structure of gut microbes in different seasons perform specific metabolic functions, and this change may be an important adaptation for T. roborowskii to cope with dietary shifts and improve energy acquisition. Our study will provide a theoretical basis for exploring the adaptive evolution to special frugivorous behavior of the T. roborowskii, which is an important supplement to the study of the gut microbiology of desert lizards.