Mitochondrial DNA analyses were carried out in order to determine the haplogroups of 6 individuals obtained from the cemetery of Resuloğlu and dated to the Early Bronze Age (EBA III). The individuals to be included in the bioinformatics analysis were evaluated according to their sequence quality and it was decided that 3 individuals could be used in further analysis. Using bioinformatics tools, it was determined that three individuals belonged to the T2e+152, H32 and JT haplogroups. These results support a link between the origins of the present-day European population and the farmers of the Anatolian Neolithic period. Furthermore, a detailed analysis of single nucleotide polymorphisms revealed T16189C and C150T mutations in the two of three individuals, which are associated with the risk of melanoma and cervical cancer - HPV infection. These molecular findings are consistent with the health profiles of the excavated skeletons, which indicate that the community struggled with infectious and metabolic diseases. The entire study was carried out in the Ancient DNA and Metagenomics Research Laboratory of the Department of Molecular Biology and Genetics, Istanbul University. Keywords: Ancient DNA, Mitochondrial DNA, Single Nucleotide Polymorphism, Haplogroup

The use of remote sensing to monitor animal populations has greatly expanded during the last decade. Drones (i.e. Unoccupied Aircraft Systems or UAS) provide a cost- and time-efficient remote sensing option to survey animals in various landscapes and sampling conditions. However, drone-based surveys may also introduce counting errors, especially when monitoring mobile animals. Using an agent-based model simulation approach, we evaluated the error associated with counting a single animal across various drone flight patterns under three animal movement strategies (random, directional persistence, and biased towards a resource) among five animal speeds (2, 4, 6, 8, 10 m/s). Flight patterns represented increasing spatial independence (ranging from lawnmower pattern with image overlap to systematic point counts). Simulation results indicated that flight pattern was the most important variable influencing count accuracy, followed by the type of animal movement pattern, and then animal speed. A lawnmower pattern with 0% overlap produced the most accurate count of a solitary, moving animal on a landscape (average count of 1.1 ± 0.6) regardless of the animal’s movement pattern and speed. Image overlap flight patterns were more likely to result in multiple counts even when accounting for mosaicking. Based on our simulations, we recommend using a lawnmower pattern with 0% image overlap to minimize error and augment drone efficacy for animal surveys. Our work highlights the importance of understanding interactions between animal movements and drone survey design on count accuracy to inform the development of broad applications among diverse species and ecosystems.

Multiple cues are often used for mate choice in complex environments, potentially entailing mismatches between different sources of information. We address the consequences thereof for receivers using the spider mite Tetranychus urticae, in which virgin females are highly valuable mates compared to mated females, given first male sperm precedence. Accordingly, males prefer virgins and distinguish them using cues from the females and/or that are present on the substrate. Whereas the former are more reliable, the latter may allow for a faster or more long-distance response. However, there can be mismatched information between cues as females move and/or mate. Here, we tested the consequences thereof by exposing males to mated or virgin females on patches previously impregnated with cues deposited by females of either mating status. Male mating attempts were solely affected by substrate cues while female acceptance and the number of mating events were independently affected by both cues. Copulation duration, in contrast, depended mainly on the mating status of the female, with the number of copulations and the total time spent mating being intermediate in environments with mismatched information. Ultimately, male survival costs mirrored male investment in mating. These results suggest that, in environments with mismatched information, the substrate cues left by females are instrumental for males to find their mates, but they can also lead to males paying survival costs without the associated benefit of mating effectively, or suffering reduced costs at the expense of losing effective mating opportunities. The benefit of using multiple cues will then hinge upon the frequency of information mismatch, which itself should vary with the dynamics of populations.

Puerto Rico harbors a diverse vertebrate fauna with high levels of endemism. However, while several books for vertebrate diversity and local checklists for birds have been published, checklists of amphibians, reptiles, and bats are lacking or nonexistent at both local and regional scales. In this study, we documented the amphibian, reptile, and bat faunas at Mata de Plátano Field Station and Nature Reserve, in Arecibo, Puerto Rico. We document four species of amphibians, seven lizards, three snakes, and nine bats. Despite prior works using samples from this nature reserve, this represents the first vertebrate checklist for the Mata de Plátano Field Station and Nature Reserve. We provide additional natural history observations based on our survey results and highlight the importance of including local and regional checklists of species for downstream research and conservation.

Rubber tree powdery mildew, a major fungal leaf disease of Heveae brasiliensis trees caused by obligate parasitic fungi (Erysiphe quercicola), is among the most important diseases affecting rubber planting areas worldwide. Phyllosphere microbiomes are currently a new research hotspot in molecular ecology, and their biological community is extremely rich. This study used high-throughput sequencing and other molecular techniques to analyze the structure and diversity of dominant fungi and bacteria in the communities of rubber tree leaves (N=16) in four representative rubber-producing regions in Hainan Province, China, after the occurrence of white powder disease. The sampled area had high species richness and stable biodiversity. This study mainly focused on (i) the dominant bacterial and fungal phyla and genera of the sampled regions; (ii) differences in the phyllosphere microbial community structure and relative abundance between healthy leaves and powdery mildew Level 3-diseased leaves within the same region; and (iii) differences in the phyllosphere microbial community structure and relative abundance between healthy leaves and diseased leaves, as well as their correlations with environmental factors, in different regions. This work is innovative in three respects: (i) distinguishing the dominant populations of phyllosphere microbes for rubber trees with powdery mildew via high-throughput detection technology to determine the impact of powdery mildew on these microbes; (ii) exploring the effects of pathogenic bacteria on phyllosphere microbes and hosts from a relatively macro perspective; and (iii) investigating the effects on phyllosphere microbial communities before and after the infection of obligatory parasite leaf pathogenic bacteria. This project is among the first conducted in China’s representative rubber-producing areas to study Erysiphe’s influence on rubber tree leaf microorganisms. These findings provide data support to better understand the biological evolution of powdery mildew diseases and establish new strategies for their ecological control in rubber tree plantations.

Recreational boats are common in many coastal waters, yet their effects on cetaceans and other sensitive marine species remain poorly understood. To address this knowledge gap, we used drone videos to quantify how harbour porpoises (Phocoena phocoena) responded to a small motorboat approaching at different speeds (10 or 20 knots). The experiment was carried out in shallow waters near Funen, Denmark (55.51° N, 10.79° E) between July and September 2022. Porpoises moved further away from the boat path during approaches at both boat speeds. In addition, porpoises swam faster when approached at 20 knots but not when approached at 10 knots, and they had a higher likelihood of moving away from the boat path when approached at 10 knots but not at 20 knots. Importantly, the received sound level did not depend on how fast the boat approached, suggesting that differences in porpoise responses were related to the speed of the boat’s approach rather than to sound itself. The porpoises’ behaviour during the minute where the boat was closest did not differ from their behaviour before boat exposure, indicating that the direct impact of small vessels on porpoise behaviour was most likely small. Nevertheless, repeated exposure to noise from small vessels could influence porpoises’ foraging efforts and cause them to relocate from disturbed areas. The approach used in this study increases our understanding of recreational boats’ impact on harbour porpoises and can be used to inform efficient mitigation measures to help conservation efforts.

As DNA sequencing technology continues to rapidly improve, studies investigating the microbial communities of host organisms (i.e., microbiomes) are becoming not only more popular but also more financially accessible. Across many taxa, microbiomes can have important impacts on organismal health and fitness. To evaluate the microbial community composition of a particular microbiome, microbial DNA must be successfully extracted. Fecal samples are often easy to collect and are a good source of gut microbial DNA. Additionally, interest in the avian preen gland microbiome is rapidly growing, due to the importance of preen oil for many aspects of avian life. Microbial DNA extractions from avian fecal and preen oil samples present multiple challenges, however. Here, we describe a modified PrepMan Ultra Sample Preparation Reagent microbial DNA extraction method that is less expensive than other commonly used methodologies and is highly effective for both fecal and preen oil samples collected from a broad range of avian species. We expect our method will facilitate microbial DNA extractions from multiple avian microbiome reservoirs, which have previously proved difficult and expensive. Our method therefore increases the feasibility of future studies of avian host microbiomes.

The lack of recovery of Chinook salmon (Oncorhynchus tshawytscha) in the Pacific Northwest has been blamed in part on predation by pinnipeds, particularly the harbor seal (Phoca vitulina). Previous work at a limited number of locations has shown that male seal diet contains more salmon than that of female seals and that sex ratios at haul-out sites differ spatiotemporally. This intrapopulation variation in predation may result in greater effects on salmon than suggested by models assuming equal spatial distribution and diet proportion. To address the generality of these patterns, we examined the sex ratios and diet of male and female harbor seals from 13 haul-out sites in the inland waters of Washington State and the province of British Columbia during 2012-2018. DNA metabarcoding was conducted to determine prey species proportions of individual scat samples. The sex of harbor seals was then determined from each scat matrix sample with the use of quantitative polymerase chain reaction. We analyzed 2,045 harbor seal scat samples using Generalized Linear Mixed Models (GLMMs) to examine the factors influencing harbor seal sex ratio at haul-out sites and permutational multivariate analysis of variance (PERMANOVA) to examine the influence of sex and haul-out site on harbor seal diet composition. We found that the overall sex ratio was 1:1.02 (female:male) with notable spatiotemporal variation. Salmoniformes were about 2.6 times more abundant in the diet of males than females, and Chinook salmon comprised ca. three times more of the average male harbor seal’s diet than the average female’s diet. Based on site-specific sex ratios and diet data, we identified three haul-out sites where Chinook salmon appear to be under high predation pressure by male harbor seals. Our study indicates that combining sex-specific pinniped diet data with the sex ratio of haul-out sites can help identify priority sites of conservation concern.

Exploring the geological events and climate change in the Himalaya-Hengduan Mountains (HHM) region and the Qinghai-Tibet Plateau (QTP) is crucial for understanding the impact of environmental change on biogeographic distribution and biological evolution. To delve deeper into these mechanisms, we reconstructed the evolutionary history of three Notholirion species that span these regions. Here, we examined a total of 254 individuals from 31 populations of these three species, utilizing five chloroplast DNA (cpDNA) (matK, ndhA, ndhG-ndhI, petB-petD, and petL-petG), along with one nuclear DNA region (internal transcribed spacer, ITS). We identified 14 haplotypes from cpDNA and 27 haplotypes from the ITS, each specific to corresponding species. Robust haplotype trees were detected, and obvious discrepancies were found between the cpDNA and ITS trees. A total of 147 chloroplast genomes were used for divergence time estimation, of which 10 chloroplast genomes from distinct populations of Notholirion species provided a comprehensive representation of the genus. The divergence time estimation results suggested that species of Notholirion genus originated in the southern Himalayan region during the Late Oligocene period (25.05 Ma), and the three Notholirion species then diverged during the Late Pliocene period (7.43 Ma). Our maximum model forecasts that the overall distribution range of Notholirion over four different periods remains relatively stable，from LIG to the future. The origin of the genus Notholirion was triggered by sustained climate fluctuations during the Late Oligocene, with the uplift of the Himalayas and the subsequent orogenic movements intensifying climate changes and further promoting the species divergence of Notholirion. A long evolutionary history, coupled with sexual reproduction and habitat fragmentation, likely contributed to the higher genetic diversity of Notholirion. The higher genetic differentiation among Notholirion populations may be attributed to drastic changes in the external environment within their range, as well as their constrained capacity for seed production and dispersal.

Urbanization alters ecosystems, fragmenting natural habitats, and hence, increasing isolation between populations. Therefore, a reduction in gene flow among isolated populations is expected with greater distance and time since fragmentation. Changes in the structure, density, or community composition in the remaining habitats often result in species‘ modifications of vocalizations and morphological traits. However, the relationship between genetic, vocalizations and morphological divergence in urban areas over time remains poorly understood. We analyzed ten years of genetic, acoustic, and morphological data from isolated populations of the white-eared ground-sparrow. We used seven microsatellites (SSRs), recorded, and measured five acoustic traits, and measured six morphological traits, and compared them over a period of ten years. We found an increase in inbreeding, increase in song duration, number of elements, and frequency of maximum amplitude, but a reduction in female body size and changes in male beak. However, we only identified a significant correlation between genetic diversity and the acoustic characteristics of song.

Eusocial insects, such as ants and termites, are characterized by high levels of coordinated social organization. This is contrasted by solitary insects, which display more limited forms of collective behavior. It has been hypothesized that this gradient in socio-behavioral sophistication is positively correlated with chemical profile complexity, due to a potentially increased demand for diversity in chemical communication mechanisms in insects with higher levels of social complexity. However, this claim has rarely been assessed empirically. Here, we compare different levels of chemical and transcriptomic complexity in selected species of the order Blattodea that represent different levels of social organization, from solitary to eusocial. We primarily focus on cuticular hydrocarbon (CHC) complexity, since it has repeatedly been demonstrated that CHCs are key signaling molecules conveying a wide variety of chemical information in solitary as well as eusocial insect species. We assessed CHC complexity and divergence between our studied species of different social complexity levels as well as the differentiation of their respective repertoires of CHC biosynthesis gene transcripts. Surprisingly, we did not find any consistent pattern of chemical complexity correlating with the degree of social complexity, nor did the overall chemical divergence or transcriptomic repertoire of CHC biosynthesis genes reflect on the levels of social complexity. Our results challenge the assumption that increasing social complexity is generally reflected in more complex chemical profiles and point towards the need for a more cautious and differentiated view on correlating complexity on a chemical, genetic, and social level.

We selected 15 sheep-grazed sand pastures along increasing grazing intensity to study fine scale biomass patterns of main fractions (green biomass, litter) and that of plant species and functional groups (life forms and social behaviour types). We classified them into five grazing intensity levels based on stocking rate, proximity to drinking and resting places, and the number of droppings and other tracks of grazing animals. We formulated three study questions: i) How does increasing intensity of sheep grazing affect the amount of green biomass, species richness and their relationship in sand pastures? ii) How does increasing intensity of sheep grazing affect the biomass of perennial and short-lived graminoids and forbs? iii) How does disturbance value (expressed in the biomass ratio of disturbance tolerant and ruderal species) change along the gradient of grazing intensity? A unimodal relationship between green biomass and species richness was detected. Along the grazing intensity gradient, we found an increasing trend for species richness; significant differences for green biomass (decreasing trend) and litter (decreasing trend), moreover for graminoids (decreasing trend), and short-lived forbs (increasing trend). We found an increasing amount of disturbance tolerant and ruderal species with increasing grazing intensity. We concluded that stocking rate and proximity to drinking and resting places jointly affected vegetation and created an uneven pattern for composition and amount of biomass in all grazing intensity levels. Our findings might be instructive for pastures in densely populated regions which are prone to the encroachment of disturbance-tolerant and ruderal species.

Ten state wildlife management agencies in the United States, including six within the Southeast, have delayed their spring wild turkey (Meleagris gallopavo) hunting season since 2017 by five or more days to address concerns related to the potential effects of hunting on wild turkey seasonal productivity. One hypothesis posits that if the spring hunting season is too early, there may be insufficient time for males to breed hens before being harvested, thus leading to reduced seasonal productivity. We conducted an experiment to determine if delaying the wild turkey hunting season by two weeks in south-middle Tennessee would affect various reproductive rates. In 2021 and 2022, the Tennessee Fish and Wildlife Commission experimentally delayed the spring hunting season to open 14 days later than the traditional date (the Saturday closest to 1 April) in Giles, Lawrence, and Wayne counties. We monitored reproductive rates from 2017 to 2022 in these three counties as well as two adjacent counties, Bedford and Maury, that were not delayed. We used a Before-After-Control-Impact design to analyze the proportion of hens nesting, clutch size, hatchability, nest success, poult survival, and hen survival with linear mixed-effect models and AIC model selection to detect relationships between the 14-day delay and reproductive parameters. We detected no relationship (P > 0.05) between the 14-day delay and any individual reproductive parameter. The traditional Tennessee start date had been in place since 1986 while the turkey harvest increased exponentially and more recently stabilized. Our data indicate that moving the start of the hunting season from a period prior to peak nest initiation to two weeks later to coincide with peak nest initiation and the onset of incubation resulted in similar levels of productivity in wild turkey flocks in south-middle Tennessee.

Water availability regulates plant community dynamics but the drought response of seedlings remains poorly known despite their vulnerability, especially for the Asian tropics. In particular, discerning how functional traits of seedlings mediate drought response can aid generalizable predictions of tree responses to global environmental change. We assessed interspecific variation in drought response explained by above- and below-ground seedling traits. We conducted a dry-down experiment in the greenhouse using 16 tree species from the humid forests of Western Ghats in southern India, chosen to represent differences in seasonality affiliations–sites of high and low seasonal drought. We compared seedling survival, growth, and photosynthetic performance under drought and well-watered conditions, and assessed the extent to which species responses were explained by seasonality affiliation and 12 traits of root, stem and leaf. We found that the species from seasonally dry forest reduced photosynthetic rate in drought compared to well-watered conditions, but seasonality affiliation did not explain differences in growth and survival. Performance changes in drought vs well-watered conditions were best explained by anatomical traits of xylem, veins and stomata. Species with larger xylem reduced their growth and photosynthesis to tolerate desiccation. In drought, species with smaller stomata showed reduced survival even though photosynthetic activity decreased by a larger extent with larger stomata. Our study shows that anatomical traits related to xylem and stomata, directly related to water transport and gas-exchange, played a more prominent role than commonly used soft traits (e.g., specific leaf area, wood density) in explaining species response to drought, and may offer a better proxy for physiological traits related to drought tolerance of seedlings.

A unique new species, Oreocharis scutifolia Z. Xie, Miao Zhang & H. H. Kong, endemic to the Dry and Hot Valley of Jinsha River Basin, Yunnan, China, is described and illustrated here. It is similar to O. cordatula (Craib) Pellegr. and O. aurantiaca Baill. in some morphological characters, but differs in its unique peltate, ovate to oblong leaf blades with emarginated apex, places and types of indumentum, length of peduncles and corolla, also have significant differences in these species. Molecular phylogenetic analysis based on transcriptome data strongly supported O. scutifolia as a new species, while it forms a sister group with O. henryana Oliv., O. cordatula (Craib) Pellegr., O. minor Pellegr. and O. aurantiaca Baill. (ML = 100). Due to its tiny population, narrow distribution range, and the serious threat from human activities, invasive plants and damaged habitat, the new species is assessed as “critically endangered” following the IUCN categories and criteria.

Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here we conduct a literature review examining temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation rate. We find that there is wide room for improvement in sharing code, as scientists are overwhelmingly (95%) failing to publish their code and that there has been no significant improvement over time. We also determined that there is a significant incentive to share, as we additionally find that code sharing can considerably improve citations, particularly when combined with open-access publication.

Leucism, in which pigmentation is lost over part or the entire body of an animal, has a range of possible genetic causes. Here, we report leucism in an individual tiger keelback (Rhabdophis tigrinus) found on Jeung Island, Shinan-gun, Jeollanam-do, South Korea, during a survey of the distribution of reptiles in the area. The individual was observed sunbathing in the bushes next to a pond. This individual exhibited ecdysis, thus it considered that have normal feeding activity. Our report represents the first observation of leucism in R. tigrinus, and thus, further analysis is needed of this phenotype to more clearly understand its impact on the species and its natural history.

Coat colour and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare colour variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare colour variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare colour variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of colour variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 colour-variable species and 59 rare colour variants. In 17 variable phenotypic populations for which genetic diversity was available, the average AR was 4.18, HO = 0.59, and HE = 0.66, and FIS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare colour variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare colour variants could be added to the list of phenotypic consequences of inbreeding in the wild.