Bird diversity has declined as native birds have avoided using the green desert after the Smooth Cordgrass Spartina alterniflora invaded coastal China. After many years of coexistence, a few passerine birds began to enter and use Smooth Cordgrass, but only birds of nonspecialised habitat. In this study, we first found that a native reed-specific bird, the Parrotbill Calamornis heudei, flocked and sang in a Smooth Cordgrass habitat in the whole overwintering period near Sheyang Port in Yancheng, Jiangsu Province. This phenomenon indicates that native obligate birds may be forced to adapt to exotic Smooth Cordgrass habitats after long-term coexistence; obviously, the distribution, feeding and reproduction of birds would be affected. Is this an ecological trap? Which may lead to unknown ecological consequences. We suggest that more research attention should be given to this process occurring along the Chinese coast.

Local adaptation to annually changing environments has evolved in numerous species. Seasonal coat colour change is an adaptation that has evolved in multiple mammal and bird species occupying areas that experience seasonal snow cover. It has a critical impact on fitness as predation risk may increase when an individual is mismatched against its habitat’s background colour. In this paper we investigate the impact of landscape covariates on moult timing in a native winter-adapted herbivore, the mountain hare (Lepus timidus), throughout Norway. Data was collected between 2011 and 2019 at 678 camera trap locations deployed across an environmental gradient. Based on this data, we created a Bayesian multinomial logistic regression model that quantified the correlations between landscape covariates and coat colour phenology and analysed among season and year moult timing variation. Our results demonstrate that mountain hare moult timing is strongly correlated with altitude and latitude with hares that live at higher latitudes and altitudes keeping their winter white coats for longer than their conspecifics that inhabit lower latitudes and altitudes. Moult timing was also weakly correlated with climate zone with hares that live in coastal climates keeping their winter white coats for longer than hares that live in continental climates. We found evidence of some among year moult timing variation in spring, but not in autumn. We conclude that mountain hare moult timing has adapted to local environmental conditions throughout Norway.

Ontogenetic color change in animals is an interesting evolution-related phenomenon that has been studied by evolutionary biologists for decades. However, the performance of quantitative and continuous color measurements throughout the life cycle of animals is a challenge. To understand the rhythm of change in tail color and sexual dichromatism, we used a spectrometer to measure the tail color of blue-tailed skink (Plestiodon elegans) from birth to sexual maturity. Lab color space was selected due to its simple, fast, and accurate and depends on the visual sense of the observer for measuring the tail color of skinks. A strong relationship was observed between color indexes (values of L*, a*, b*) and growth time of skink. The luminance of tail color decreased from juveniles to adults in both sexes. Moreover, we observed differences in color rhythms between the sexes, which may be influenced by different behavioral strategies employed by them. This study provides continuous measurements of change in tail color in skinks from juveniles to adults and offers insights into their sex-based differences. Our findings explain the potential factors that drive dichromatism between the sexes of lizards and is expected to serve as a reference for future studies that explore possible mechanisms of ontogenetic color change in reptiles.

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.

Tetraodontiformes is a special group of higher teleosts, with a long and problematic taxonomic history due to their wide distribution and species diversity. It is a difficult task for both professionals and nonprofessionals to accurately identify all species only according to morphological characteristics. DNA barcoding can identify species at the molecular level. In this study, we collected 616 specimens of Tetraodontiformes and their DNA barcodes from the coastal waters of China. According to the morphological characteristics, 50 species were preliminarily identified, belonging to 23 genera, 6. Among them, DNA barcoding analysis showed that Takifugu pseudommus and Takifugu chinensis are the synonyms of Takifugu rubripes. And Lagocephalus wheeleri is the synonym of Lagocephalus Spadiceus. The third important finding is that the species of Takifugu have close genetic relationship. If T. rubripes, T. pseudommus and T. chinensis are taken as one species, the average interspecific genetic distance of Takifugu is 6.21 times of the average intraspecific genetic distance, which does not reach the DNA barcode threshold of more than 10 times proposed by Hebert. Among them, the genetic distance between T. oblongus and T. stictonotus is the largest, 0.045; And between T. bimaculatus and T. flavidus is the smallest, only 0.013. However, species can be clustered into separate clades in the NJ tree. In conclusion, this study provided molecular basis for solving the problem of confusion in the classification of Tetraodontiformes, it found that there are synonym phenomena in the order, and provided molecular evidence for clarifying the valid species names of Lagocephalus Spadiceus and Takifugu rubripes. The results can provide reliable DNA barcoding information for the identification and classification of Tetraodontiformes, and also provide technical support for the development and utilization of puffer fish resources and the identification of the original components of related commodities on the aquatic product market.

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.

A document by Jana Ebersbach. Click on the document to view its contents.

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.

In the Anopheles genus, various mosquito species are able to transmit Plasmodium parasites responsible for malaria, while others are non-vectors. In an effort to better understand the biology of Anopheles species and to quantify transmission risk in an area, the identification of mosquito species collected on the field is an essential but problematic task. Morphological identification requires expertise, well-preserved specimens and high-quality equipment, and it does not allow any subsequent verification when samples are later used in a destructive treatment. Moreover, it involves physical manipulations that are not compatible with experiments requiring fast sampling and processing of specimens, hence species identification is often based on DNA sequencing of reference genes or region such as the Internal Transcribed Spacer 2 (ITS2) region of nuclear ribosomal DNA. Sequencing ITS2 for numerous samples is costly, but the design of species-specific PCR primers is not always possible when local species diversity is high. Here, we introduce a molecular technique of species identification based on precise determination of ITS2 length combined with a simple visual observation, the color of mosquito hindleg tip. DNA extracted from field-collected Anopheles mosquitoes was amplified with universal Anopheles ITS2 primers and analyzed with a capillary electrophoresis device, which precisely determines the size of the fragments. We defined windows of amplicon sizes combined with fifth hind tarsus color, which allow to discriminate the major Anopheles species found in our collections. We validated our parameters via Sanger sequencing of the ITS2 amplicons. This method can be particularly useful in situations with a moderate species diversity, i.e. when the number of local species is too high to define species-specific primers but low enough to avoid individual ITS2 sequencing. This tool will be of interest to evaluate local malaria transmission risk and this approach may further be implemented for other mosquito genera.

Reproductive isolation plays an important role in maintaining the species integrity of sympatric close relatives. For sympatric Arisaema species, interspecific gene flow is expected to be effectively prevented by pre-pollination barriers, particularly strong pollinator isolation mediated by fungus gnats. However, due to the lack of quantitative studies combining multiple pre- and post-pollination barriers, it is not known whether pre-pollination isolation is complete, and whether post-pollination barriers also contribute to reproductive isolation among some Arisaema species. We studied five pre- and post-pollination barriers (geographic isolation, phenological isolation, pollinator isolation, hybrid fruit production, and hybrid seed formation) among three sympatric Arisaema species (A. bockii, A. lobatum, and A. erubescens). The strength of individual barriers and their contribution to total isolation were quantified.The habitat elevations of the three Arisaema species mostly overlapped. Although phenological isolation and pollinator isolation reduced the frequencies of interspecific pollen transfer among these species, the partial overlap of flowering times and pollinator assemblages resulted in pre-pollination isolation that does not adequately prevent interspecific hybridization. Post-pollination barriers also contributed to reproductive isolation at the hybrid fruit and seed formation stages.We propose that, although pre-pollination barriers are expected to contribute more to total isolation than post-pollination barriers in Arisaema, pre-pollination barriers may not completely prevent interspecific pollen transfer among some Arisaema species. Post-pollination barriers, which are generally ignored, may also have contributed significantly to reproductive isolation in Arisaema.

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.

The development of DNA-based methods in recent decades has opened the door to numerous new lines of research in the biological sciences. While their speed and accuracy are clearly beneficial, the sensitivity of these methods has the adverse effect of increased susceptibility to false positives resulting from contamination in field or lab. Here, we present findings from a metabarcoding study on the diet of and food availability for several insectivorous birds, in which multiple lepidopteran species not known to occur locally were discovered. After describing the pattern of occurrences of these non-local species in the samples, we discuss various potential origins of these sequences. First, we assess that the taxonomic assignments appear reliable, and local occurrences of many of the species can be plausibly ruled out. Then, we look into the possibilities of natural environmental contamination, judging it to be unlikely, albeit impossible to fully falsify. Finally, while the pattern of occurrences did not suggest lab contamination, we find overlap with material handled in the same lab, which was undoubtedly not coincidental. Even so, not all exact sequences were accounted for in these locally conducted studies, nor was it clear if these and other sequences could remain detectable years later. Although the full explanation for the observations of non-local species remains inconclusive, these findings highlight the importance of critical examination of metabarcoding results, and showcase how species-level taxonomic assignments utilizing comprehensive reference libraries may be a tool in detecting potential contamination events, and false positives in general.

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.