Direct assessment of tropical tuna abundance from their associative behaviour around floating objects.

Managing populations of wild harvested species requires the ability to regularly provide accurate abundance assessments. For most marine species, changes in abundance can only be monitored indirectly, using methods reliant on harvest-based indices, with significant inherent limitations surrounding the estimation and standardization of harvest effort. Tropical tunas are some of the most exploited marine species in the world and are among several species in critical need of alternative methods for estimating abundance. Addressing this concern, we developed the Associative Behaviour-Based abundance Index (ABBI), designed to provide direct abundance estimates for animals, which exhibit an associative behaviour with aggregation sites. Its implementation in the western Indian Ocean on skipjack tuna (Katsuwonus pelamis), yellowfin tuna (Thunnus albacares) and bigeye tuna (Thunnus obesus), revealed similar trajectories in their relative abundance. The ABBI stands as a potentially promising alternative to enhance traditional tropical tuna stock assessments methods, as well as a new opportunity to assess the abundance of other wild species that display an associative behaviour with physical structures found in their natural environment.

Widespread cultural change in declining populations of Amazon parrots.

Species worldwide are experiencing anthropogenic environmental change, and the long-term impacts on animal cultural traditions such as vocal dialects are often unknown. Our prior studies of the yellow-naped amazon (Amazona auropalliata) revealed stable vocal dialects over an 11-year period (1994-2005), with modest shifts in geographic boundaries and acoustic structure of contact calls. Here, we examined whether yellow-naped amazons maintained stable dialects over the subsequent 11-year time span from 2005 to 2016, culminating in 22 years of study. Over this same period, this species suffered a dramatic decrease in population size that prompted two successive uplists in IUCN status, from vulnerable to critically endangered. In this most recent 11-year time span, we found evidence of geographic shifts in call types, manifesting in more bilingual sites and introgression across the formerly distinct North-South acoustic boundary. We also found greater evidence of acoustic drift, in the form of new emerging call types and greater acoustic variation overall. These results suggest cultural traditions such as dialects may change in response to demographic and environmental conditions, with broad implications for threatened species.

Range-wide salamander densities reveal a key component of terrestrial vertebrate biomass in eastern North American forests.

Characterizing the population density of species is a central interest in ecology. Eastern North America is the global hotspot for biodiversity of plethodontid salamanders, an inconspicuous component of terrestrial vertebrate communities, and among the most widespread is the eastern red-backed salamander, Plethodon cinereus. Previous work suggests population densities are high with significant geographic variation, but comparisons among locations are challenged by lack of standardization of methods and failure to accommodate imperfect detection. We present results from a large-scale research network that accounts for detection uncertainty using systematic survey protocols and robust statistical models. We analysed mark-recapture data from 18 study areas across much of the species range. Estimated salamander densities ranged from 1950 to 34 300 salamanders ha-1, with a median of 9965 salamanders ha-1. We compared these results to previous estimates for P. cinereus and other abundant terrestrial vertebrates. We demonstrate that overall the biomass of P. cinereus, a secondary consumer, is of similar or greater magnitude to widespread primary consumers such as white-tailed deer (Odocoileus virginianus) and Peromyscus mice, and two to three orders of magnitude greater than common secondary consumer species. Our results add empirical evidence that P. cinereus, and amphibians in general, are an outsized component of terrestrial vertebrate communities in temperate ecosystems.

Population size, HIV prevalence, and antiretroviral therapy coverage among key populations in sub-Saharan Africa: collation and synthesis of survey data, 2010-23.

BACKGROUND: Key population HIV programmes in sub-Saharan Africa require epidemiological information to ensure equitable and universal access to effective services. We aimed to consolidate and harmonise survey data among female sex workers, men who have sex with men, people who inject drugs, and transgender people to estimate key population size, HIV prevalence, and antiretroviral therapy (ART) coverage for countries in mainland sub-Saharan Africa. METHODS: Key population size estimates, HIV prevalence, and ART coverage data from 39 sub-Saharan Africa countries between 2010 and 2023 were collated from existing databases and verified against source documents. We used Bayesian mixed-effects spatial regression to model urban key population size estimates as a proportion of the gender-matched, year-matched, and area-matched population aged 15-49 years. We modelled subnational key population HIV prevalence and ART coverage with age-matched, gender-matched, year-matched, and province-matched total population estimates as predictors. FINDINGS: We extracted 2065 key population size data points, 1183 HIV prevalence data points, and 259 ART coverage data points. Across national urban populations, a median of 1·65% (IQR 1·35-1·91) of adult cisgender women were female sex workers, 0·89% (0·77-0·95) were men who have sex with men, 0·32% (0·31-0·34) were men who injected drugs, and 0·10% (0·06-0·12) were women who were transgender. HIV prevalence among key populations was, on average, four to six times higher than matched total population prevalence, and ART coverage was correlated with, but lower than, the total population ART coverage with wide heterogeneity in relative ART coverage across studies. Across sub-Saharan Africa, key populations were estimated as comprising 1·2% (95% credible interval 0·9-1·6) of the total population aged 15-49 years but 6·1% (4·5-8·2) of people living with HIV. INTERPRETATION: Key populations in sub-Saharan Africa experience higher HIV prevalence and lower ART coverage, underscoring the need for focused prevention and treatment services. In 2024, limited data availability and heterogeneity constrain precise estimates for programming and monitoring trends. Strengthening key population surveys and routine data within national HIV strategic information systems would support more precise estimates. FUNDING: UNAIDS, Bill & Melinda Gates Foundation, and US National Institutes of Health.

Interactive and lag effects of environmental factors on the density of schistosome-transmitting Oncomelania hupensis: A twelve-year monthly repeated survey.

Schistosomiasis is a significant public health threat, and Oncomelania hupensis is the only intermediate host for schistosoma japonicum. We conducted 12-year monthly repeated surveys to explore the interactive and lag effects of environmental factors on snail density and to monitor their long-term and seasonal trends in a bottomland around the Dongting Lake region in China. Relevant environmental data were obtained from multiple sources. A Bayesian kernel machine regression model and a Bayesian temporal model combined with a distributed lag model were constructed to analyze interactive and lag effects of environmental factors on snail density. The results indicated the average annual snail density in the study site exhibited an increasing and then decreasing trend, peaking in 2013. Snail densities were the highest in October and the lowest in January in a year. Normalized Difference Vegetation Index (NDVI) and water level were the most effective predictors of snail density, with potential interactions among temperature, precipitation, and NDVI. The mean minimum temperature in January, water level, precipitation and NDVI were positively correlated with snail density at lags ranging from 1 to 4 months. These findings could serve as references for relevant authorities to monitor the changing trend of snail density and implement control measures, thereby reducing the occurrence of schistosomiasis.

Cost Optimisation of Individual-Based Institutional Reward Incentives for Promoting Cooperation in Finite Populations.

In this paper, we study the problem of cost optimisation of individual-based institutional incentives (reward, punishment, and hybrid) for guaranteeing a certain minimal level of cooperative behaviour in a well-mixed, finite population. In this scheme, the individuals in the population interact via cooperation dilemmas (Donation Game or Public Goods Game) in which institutional reward is carried out only if cooperation is not abundant enough (i.e., the number of cooperators is below a threshold 1 ≤ t ≤ N - 1 , where N is the population size); and similarly, institutional punishment is carried out only when defection is too abundant. We study analytically the cases t = 1 for the reward incentive under the small mutation limit assumption and two different initial states, showing that the cost function is always non-decreasing. We derive the neutral drift and strong selection limits when the intensity of selection tends to zero and infinity, respectively. We numerically investigate the problem for other values of t and for population dynamics with arbitrary mutation rates.

Formation of human kinship structures depending on population size and cultural mutation rate.

How does social complexity depend on population size and cultural transmission? Kinship structures in traditional societies provide a fundamental illustration, where cultural rules between clans determine people's marriage possibilities. Here, we propose a simple model of kinship interactions that considers kin and in-law cooperation and sexual rivalry. In this model, multiple societies compete. Societies consist of multiple families with different cultural traits and mating preferences. These values determine interactions and hence the growth rate of families and are transmitted to offspring with mutations. Through a multilevel evolutionary simulation, family traits and preferences are grouped into multiple clans with interclan mating preferences. It illustrates the emergence of kinship structures as the spontaneous formation of interdependent cultural associations. Emergent kinship structures are characterized by the cycle length of marriage exchange and the number of cycles in society. We numerically and analytically clarify their parameter dependence. The relative importance of cooperation versus rivalry determines whether attraction or repulsion exists between families. Different structures evolve as locally stable attractors. The probabilities of formation and collapse of complex structures depend on the number of families and the mutation rate, showing characteristic scaling relationships. It is now possible to explore macroscopic kinship structures based on microscopic interactions, together with their environmental dependence and the historical causality of their evolution. We propose the basic causal mechanism of the formation of typical human social structures by referring to ethnographic observations and concepts from statistical physics and multilevel evolution. Such interdisciplinary collaboration will unveil universal features in human societies.

Global expansion of human-wildlife overlap in the 21st century.

Understanding the extent to which people and wildlife overlap in space and time is critical for the conservation of biodiversity and ecological services. Yet, how global change will reshape the future of human-wildlife overlap has not been assessed. We show that the potential spatial overlap of global human populations and 22,374 terrestrial vertebrate species will increase across ~56.6% and decrease across only ~11.8% of the Earth's terrestrial surface by 2070. Increases are driven primarily by intensification of human population densities, not change in wildlife distributions caused by climate change. The strong spatial heterogeneity of future human-wildlife overlap found in our study makes it clear that local context is imperative to consider, and more targeted area-based land-use planning should be integrated into systematic conservation planning.

Effect of local and regional factors on the structure of the fish communities associated with aquatic macrophyte stands in oxbow lakes on the Amazon floodplain.

The Amazon floodplain is home to an extremely high diversity of fish, with lakes playing an important role in the establishment of this biological richness. These lacustrine environments are subject to constant fluctuations caused by the annual flood pulse, with local factors and other regional patterns also contributing to the variation in fish community structure. The present study verified how local (depth and transparency of the water, the size and species composition of the macrophyte stands) and regional factors (spatial distribution of the stands and the hydrological phase) influence the structure of the fish community of the floodplain lakes of the Môa River, in northern Brazil. Fish species richness was influenced by the depth of the water and the spatial distribution of the macrophyte stands. Fish species composition was influenced by local environmental variables, spatial structure, and the hydrological phase. However, variation partitioning indicated that only the hydrological phase explained the variation in fish composition. These findings indicate that the local environment, the spatial structure, and the hydrological phase drive changes in the structure of the fish communities associated with aquatic macrophytes in the floodplain lakes of the Amazon basin.

Prevalence of bovine trypanosomosis and tsetse fly density in Loka Abaya and Derara districts in Sidama Regional State, Ethiopia.

Animal trypanosomosis is a significant livestock disease with economic and social repercussions, reducing the supply of animal products and restricting the utilization of animals for traction and transportation. In Ethiopia, it is prevalent and poses a major hindrance to the advancement of animal production. This repeated cross-sectional study was aimed at assessing seasonal variation in bovine trypanosomosis prevalence and tsetse fly density and identifying the potential risk factors in the Loka Abaya and Derara districts of the Sidama National Regional State. Blood samples were collected from 964 cattle, 484 samples during the dry season, and 480 during the wet season. The buffy coat method was employed to analyze these samples. Furthermore, 78 standard NGU traps were set up at various locations in the two districts during both seasons for entomological investigation. The overall apparent prevalence of trypanosomosis was 9% (95% CI 7.3-11.0), without a significant difference (p > 0.05) between the dry season (7.4%) and wet season (10.6%). The apparent prevalence was significantly higher in Loka Abaya (11.8%) than in Derara (6.3%) district (OR = 2.04; p = 0.003) and in cattle with black coat color (29%) than in mixed color (6.8%) (OR = 5.3; p < 0.001). The majority of infections were caused by Trypanosoma congolense (70%), followed by T. vivax (29%), and mixed infections (1%) with the two species. The average packed cell volume (PCV) was significantly (p < 0.0001) lower in infected animals (20.7 ± 4%) compared to uninfected ones (25.5 ± 5.4%), in cattle examined during the dry season (24.1 ± 6%) versus the wet season (26.1 ± 4.7%), in cattle sampled from the Loka Abaya district (24.2 ± 5.5%) versus Derara district (26 ± 5.3%), and in cattle with poor body condition (23.6 ± 5.7%) compared to those with good body condition (26.5 ± 5.3%). A total of 5282 flies were captured during the study, with 4437 (84%) being tsetse flies (Glossina pallidipes), 439 (8.3%) Tabanids, 190 (3.6%) Stomoxys spp., and 216 (4.1%) Musca spp. The apparent density (AD) of G. pallidipes was 28.4 flies/trap/day, showing no statistically significant difference between wet (32.1) and dry (24.6) seasons (p > 0.05). The AD of G. pallidipes was significantly (p < 0.001) higher in the Loka Abaya district (57.3) than in the Derara district (0.9). The study highlights a moderate trypanosomosis apparent prevalence and high AD of G. pallidipes, showing significant variation between the study districts but no seasonal difference. The observed apparent prevalence of trypanosomosis and tsetse fly density notably affects animal health and productivity. As a result, strategies for vector control like insecticide-treated targets, trypanocidal medications for infected animals, and community-based initiatives such as education and participation in control programs are recommended.

Influence of weather conditions and plant growth on populations of the solenopsis mealybug (Phenacoccus solenopsis Tinsley) infesting maize plants.

The cotton or solenopsis mealybug, Phenacoccus solenopsis (Tinsley, 1898) (Hemiptera: Pseudococcidae), infests various host plants in Egypt. A study was conducted to observe the incidence of mealybugs and the possible influences of meteorological variables and plant age on the insect population of maize (single-hybrid 168 yellow maize cultivar) plants in Esna district, Luxor governorate, Egypt, in two consecutive seasons (2021 and 2022). P. solenopsis infested maize plants from the 3rd week of June to harvest, and had three peaks of seasonal incidence/season namely; in the 1st week of June in the 3rd/4th week of July, and the 2nd week of August. Similarly, there were three peaks in the percent of infestations per season. In the first season, the average population density of P. solenopsis per sample was 174.04 ± 16.93 individuals, and in the second season, 156.72 ± 14.28 individuals. The most favorable climate for P. solenopsis population increase and infestation occurred in August in the first season and in September in the second season, while June was less suitable in both growing seasons (as estimated by weekly surveys). The combined effects of weather conditions and plant age are significantly related to the estimates of P. solenopsis populations, with an explained variance (E.V.) of 93.18 and 93.86%, respectively, in the two seasons. In addition, their influences explained differences in infestation percentages of 93.30 and 95.54%, respectively, in the two seasons. Maize plant age was the most effective factor in determining changes in P. solenopsis population densities in each season. The mean daily minimum temperature in the first season and mean daily dew point in the second season were the most important factors affecting the percent changes in infestation. However, in both seasons, the mean daily maximum temperature was the least effective variable in population and infestation variation. This study paves the way for monitoring and early detection of mealybugs in maize; as well as the optimal climatic conditions for its development.

Effects of the maternal social environment on the mating signals and mate preferences of adult offspring in Enchenopa treehoppers.

Much is known about how the maternal environment can shape offspring traits via intergenerational effects. It is less clear, however, whether such effects may reach adult offspring sexual traits, with potential consequences for sexual selection and speciation. Here, we report effects of adult female aggregation density on the mating signals and mate preferences of their offspring in an insect that communicates via plant-borne vibrational signals. We experimentally manipulated the density of aggregations experienced by egg-laying mothers, reared the offspring in standard densities, and tested for corresponding differences in their signals and preferences. We detected a strong effect in male signals, with sons of mothers that experienced low aggregation density signalling more. We also detected a weak effect on female mate preferences, with daughters of mothers that experienced low aggregation density being less selective. These adjustments may help males and females find mates and secure matings in low densities, if the conditions they encounter correspond to those their mothers experienced. Our results thus extend theory regarding adjustments to the social environment to the scale of intergenerational effects, with maternal social environments influencing the expression of the sexual traits of adult offspring.

Phlebotomine sand fly distribution and abundance in France: A systematic review.

Global changes in climate are contributing to modified Phlebotomine sand fly presence and activity, and the distribution of the pathogens they transmit (e.g., Leishmania and Phlebovirus), and are leading to their possible extension toward northern France. To predict the evolution of these pathogens and control their spread, it is essential to identify and characterize the presence and abundance of potential vectors. However, there are no recent publications describing sand fly species distribution in France. Consequently, we carried out a systematic review to provide distribution and abundance maps over time, along with a simplified dichotomous key for species in France. The review adhered to PRISMA guidelines, resulting in 172 relevant capture reports from 168 studies out of the 2646 documents retrieved, of which 552 were read and 228 analyzed. Seven species were recorded and categorized into three groups based on their abundance: low abundance species, abundant but little-studied species, and abundant vector species. Sand flies are certainly present throughout France but there is a greater diversity of species in the Mediterranean region. Phlebotomus perniciosus and Ph. ariasi are the most abundant and widely distributed species, playing a role as vectors of Leishmania. Sergentomyia minuta, though very abundant, remains under-studied, highlighting the need for further research. Phlebotomus papatasi, Ph. perfiliewi, Ph. sergenti, and Ph. mascittii are present in low numbers and are less documented, limiting understanding of their potential role as vectors. This work provides the necessary basis for comparison of field data generated in the future.

Title: Répartition et abondance des phlébotomes en France : revue systématique. Abstract: Les changements globaux du climat contribuent à modifier la présence et l'activité des phlébotomes, ainsi que la répartition des pathogènes qu'ils transmettent (par exemple Leishmania et Phlebovirus), et conduisent à leur éventuelle extension vers le nord de la France. Pour prédire l'évolution de ces pathogènes et contrôler leur propagation, il est essentiel d'identifier et de caractériser la présence et l'abondance des vecteurs potentiels. Il n'existe cependant aucune publication récente décrivant la répartition des espèces de phlébotomes en France. Par conséquent, nous avons réalisé une revue systématique pour fournir des cartes de répartition et d'abondance dans le temps, ainsi qu'une clé dichotomique simplifiée pour les espèces françaises. La revue a respecté les lignes directrices PRISMA, aboutissant à 172 rapports de capture pertinents provenant de 168 études sur les 2 646 documents récupérés, dont 552 ont été lus et 228 analysés. Sept espèces ont été recensées et classées en trois groupes en fonction de leur abondance : les espèces de faible abondance, les espèces abondantes mais peu étudiées et les espèces vectrices abondantes. Les phlébotomes sont certes présents partout en France mais on trouve une plus grande diversité d'espèces dans le bassin méditerranéen. Phlebotomus perniciosus et Ph. ariasi sont les espèces les plus abondantes et les plus largement réparties, jouant un rôle de vecteurs de Leishmania. Sergentomyia minuta, bien que très abondant, reste sous-étudié, ce qui souligne la nécessité de recherches plus approfondies. Phlebotomus papatasi, Ph. perfiliewi, Ph. sergenti et Ph. mascittii sont présents en faibles nombres et sont moins documentés, ce qui limite la compréhension de leur rôle potentiel en tant que vecteurs. Ce travail fournit la base nécessaire pour la comparaison des données de terrain générées à l'avenir.

Social, not genetic, programming of development and stress physiology of a colonial seabird.

Phenotypic differences often stem from genetic/maternal differences and/or early-life adaptations to local environmental conditions. In colonial animals, little is known on how variation in the social environment is embedded into individual phenotypes, nor what the consequences are on individual fitness. We conducted an experimental cross-fostering study on king penguins (Aptenodytes patagonicus), exchanging eggs among 134 pairs breeding in high-density (67 pairs) or low-density (67 pairs) areas of the same breeding colony. We investigated differences in parent and chick phenotypes and survival in relation to the density of their origin and foster environment. Adults breeding in colony areas of high density exhibited decreased resting behaviour and increased aggression and vigilance, increased hypometabolism during incubation fasts, and more moderate corticosterone responses shaped by exposure to chronic stressors (e.g. constant aggression by neighbours). Chick phenotypes were more influenced by the environment in which they were raised than their genetic/maternal origin. Chicks raised in high-density colonial environments showed enhanced weight gain and survival rates regardless of the density of their genetic parents' breeding areas. Our study experimentally shows advantages to breeding in colonial areas of higher breeder densities in king penguins, and highlights the importance of social settings in shaping phenotype expression in colonial seabirds.

Enhancing the accuracy and efficiency of Pacific walrus (Odobenus rosmarus divergens) surveys: A comparison of visual and aerial imagery-based counts at coastal haulouts.

This study presents a semi-automated approach utilizing unoccupied aerial vehicle (UAV) surveys to accurately estimate the abundance of Pacific walruses at large coastal haulouts in Chukotka, Russia. Seven major haulout sites were surveyed during the summers and falls of 2017-2019. Walrus counts were performed using three distinct methods: traditional visual land-based counts, complete head counts utilizing georeferenced UAV imagery, and counting walruses within model polygons within the haulout outline and employing various extrapolation techniques to predict walrus abundance across the haulout area. The results indicated that traditional visual counts neither yielded consistent results nor allowed for uncertainty estimation, unlike the site- and date-specific direct extrapolation method and the non-specific linear regression model. These latter methods consistently provided estimates, on average, within 5% of the "true" abundance determined through complete photo-based head counts. Beside yielding accurate estimates, these semi-automated methods significantly reduced counting time by at least 63%, in contrast to complete head counts. The non-specific model, which allowed the estimation of walrus abundance based on the type of the terrain and the haulout area was less accurate compared with site and date specific estimates, but provided a tool to estimate abundance when no field visits are conducted, e.g., by using high-resolution satellite imagery to measure haulout area. This model revealed that the haulouts located on flat sandy beaches exhibited mean walrus densities approximately 30.5% times higher than those on rocky shores surrounded by cliffs: 0.879 (SD = 0.1302) and 0.648 (SD = 0.1753) walrus per m2 correspondingly. The estimated daily walrus abundance at major Chukotkan haulouts in 2017-2019 ranged between 15 and 94,660 (mean = 10,397, SD = 14,477) walruses with the maximum seasonal abundances reported at Cape Serdtse-Kamen as 94,960 on 10-Oct-2017, 26,850 on 10-Oct-2018, and 87,595 on 10-Oct-2019.

Abundance-diversity relationship as a unique signature of temporal scaling in the fossil record.

Species diversity increases with the temporal grain of samples according to the species-time relationship (STR), impacting palaeoecological analyses because the temporal grain (time averaging) of fossil assemblages varies by several orders of magnitude. We predict a positive relation between total abundance and sample size-independent diversity (ADR) in fossil assemblages because an increase in time averaging, determined by a decreasing sediment accumulation, should increase abundance and depress species dominance. We demonstrate that, in contrast to negative ADR of non-averaged living assemblages, the ADR of Holocene fossil assemblages is positive, unconditionally or when conditioned on the energy availability gradient. However, the positive fossil ADR disappears when conditioned on sediment accumulation, demonstrating that ADR is a signature of diversity scaling induced by variable time averaging. Conditioning ADR on sediment accumulation can identify and remove the scaling effect caused by time averaging, providing an avenue for unbiased biodiversity comparisons across space and time.

A method to estimate prey density from single-camera images: A case study with chinstrap penguins and Antarctic krill.

Estimating the densities of marine prey observed in animal-borne video loggers when encountered by foraging predators represents an important challenge for understanding predator-prey interactions in the marine environment. We used video images collected during the foraging trip of one chinstrap penguin (Pygoscelis antarcticus) from Cape Shirreff, Livingston Island, Antarctica to develop a novel approach for estimating the density of Antarctic krill (Euphausia superba) encountered during foraging activities. Using the open-source Video and Image Analytics for a Marine Environment (VIAME), we trained a neural network model to identify video frames containing krill. Our image classifier has an overall accuracy of 73%, with a positive predictive value of 83% for prediction of frames containing krill. We then developed a method to estimate the volume of water imaged, thus the density (N·m-3) of krill, in the 2-dimensional images. The method is based on the maximum range from the camera where krill remain visibly resolvable and assumes that mean krill length is known, and that the distribution of orientation angles of krill is uniform. From 1,932 images identified as containing krill, we manually identified a subset of 124 images from across the video record that contained resolvable and unresolvable krill necessary to estimate the resolvable range and imaged volume for the video sensor. Krill swarm density encountered by the penguins ranged from 2 to 307 krill·m-3 and mean density of krill was 48 krill·m-3 (sd = 61 krill·m-3). Mean krill biomass density was 25 g·m-3. Our frame-level image classifier model and krill density estimation method provide a new approach to efficiently process video-logger data and estimate krill density from 2D imagery, providing key information on prey aggregations that may affect predator foraging performance. The approach should be directly applicable to other marine predators feeding on aggregations of prey.

Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years.

Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.

Endangered bird species of one of the last remnants of lowland Atlantic Forest in Rio de Janeiro state, Brazil: pressures and preservation measures.

The lowland Atlantic Forest, at altitudes of below 500 m, is highly fragmented, and is home to many threatened species of birds. The Brazilian state of Rio de Janeiro has a high concentration of threatened birds in the Americas and is an important residual of the dense ombrophilous formations of the Atlantic Forest, which includes the Reserva Biológica União, a high priority area for conservation of Atlantic Forest birds. This study compiled empirical and secondary records of threatened birds in this reserve and discusses potential factors determining their local occurrence. Since 2008, regular observations, including transect surveys and mist-netting, in addiction to secondary data, have provided records of 306 bird species, of which 49 appear on red lists at some level (state, national or global), including 34 listed as endangered, of which 13 are listed globally, eight of them dependent on well-conserved lowland rainforest. Future studies should include new areas of the reserve, with the aim of confirming the presence of additional threatened species. The long-term conservation of this fauna will depend not only on the adequate management of the reserve, but also the reestablishment of its connectivity with adjacent forest fragments and upland areas in the state.