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To ensure the success of genetic rescue, we must minimise the potential negative effects of outbreeding depression that may arise from selecting source populations. The difficulty in assessing the likelihood of outbreeding depression has hindered its consideration in endangered species conservation. However, genomic research offers feasible indications. Here, we conduct conservation genomic analyses on the East Asian (EA) population and the relict Western/Central Asian (WCA) population of the critically endangered Siberian crane (Leucogeranus leucogeranus). We aim to assess genetic rescue's potential advantages and disadvantages between the two populations. Our analysis shows genomic evidence of limited genetic differentiation between them. The persistent decline in population size due to historical climatic oscillations leads to a decrease in genetic diversity and an increase in inbreeding. The WCA population has excessive deleterious homozygous mutations than the EA population, suggesting suffering from inbreeding depression resulting from less effective purifying selection. Forward simulations support the increase in genetic load due to elevated levels of inbreeding compromises fitness during population collapse. We strongly recommend an urgent genetic rescue for the WCA population through population supplementation from the EA population. However, the continuous monitoring of fitness outcomes is required through captive breeding. This work provides useful insights into the genetic management of a critically endangered species and emphasises the importance of evaluating the likelihood of outbreeding depression through genomic approaches. [ABSTRACT FROM AUTHOR]

Aim: Recent literature is unveiling more complex responses of biodiversity to Pleistocenic climatic oscillations than those derived from initial models based solely on southern glacial macrorefugia. Here, we zoom in to delve into the genetic diversity and population structure of Podarcis lusitanicus, a lizard species native to the north‐western Iberian Peninsula. Location: North‐western Iberian Peninsula. Taxon: Podarcis lusitanicus. Methods: Utilising a comprehensive multilocus approach, we explored the species' phylogeography and demographic history at a very fine spatial scale and timeframe. Concurrently, we evaluated both current and historical habitat suitability for the species, linking it to the observed demographic trends. We examined DNA sequences from two mitochondrial (cytb and ND4) and three nuclear genes (ACM4, MC1R and PDC) in 230 specimens collected from 21 populations spanning most of the species' distribution range. Results: Our findings corroborate cytonuclear discordances in Podarcis, with nuclear genes failing to identify the mitochondrial clades in P. lusitanicus. Despite its separation from other Podarcis species approximately 4 million years ago, its diversification occurred much more recently, around 0.4 million years ago, resulting in three monophyletic lineages that are geographically coherent. This pattern suggests that some lineages of P. lusitanicus might have gone extinct after the split from the common ancestor. Pleistocene climatic oscillations profoundly influenced the demographic history of the species. During warmer periods, such as the Last Interglacial, populations expanded and came into secondary contact, whereas during the Last Glacial Maximum, populations contracted and became isolated in multiple micro‐refugia. The subsequent Mid‐Holocene warming facilitated population recovery, range expansion and lineage admixture. Main Conclusions: This study underscores the intricate interplay between isolation and dispersal at a microscale, driven by Pleistocene climatic fluctuations, which have profoundly shaped the genetic structure and diversity of Iberian terrestrial biodiversity and may remain overlooked by biogeographic studies at coarser scales. [ABSTRACT FROM AUTHOR]

Recent advances in whole-genome sequencing technologies have shown potential for establishing a genomic-level evolutionary process framework for avian species. In this study, a comprehensive whole-genome resequencing approach was employed to generate genome-wide data from 12 individuals of Temminck’s tragopan (Tragopan temminckii), a species under imminent threat and experiencing rapid decline due to habitat fragmentation and loss in China. Population genomic analyses indicated significant genetic diversity and increased linkage disequilibrium in Temminck’s tragopan, despite habitat fragmentation. It was further suggested that the historical population dynamics of Temminck’s tragopan from the western Sichuan Plateau was influenced by glacial climatic events and anthropogenic activities. Furthermore, male-specific developmental pathways, particularly those related to the androgen receptor and associated genes, were found to contribute to the observed sexual dimorphism in Temminck’s tragopan. These findings establish a preliminary basis for comprehending the evolutionary dynamics of Temminck’s tragopan. [ABSTRACT FROM AUTHOR]

Globally, 60% of species in the order Psittaciformes are experiencing population declines. Understanding demographic and health trends in populations is vital for the prioritisation of limited conservation resources. The Cape Parrot Poicephalus robustus is a South African endemic forest species that is endangered by habitat degradation and Psittacine Beak and Feather Disease (PBFD). In the Amathole region of the Eastern Cape province, Cape Parrots gather in large numbers every autumn to feed at a particular orchard of Pecan trees Carya illinoinensis. This annual event is an opportunity for researchers to assess trends in a population that does not otherwise typically form large flocks. We used a novel, non-invasive method of flock photography analysis between 2017 and 2022 to assess the demographics and PBFD symptoms of the population. A mean of 439 ± SD 127 Cape Parrots visited the orchard on the peak day each year, with 1.2 males per female and 3 adults per juvenile overall. Proportions of juveniles fluctuated between extremes of 70% in 2019 and < 4% in 2020. PBFD symptoms increased markedly in the food-scarce year of 2019, with a gradual recovery seen in the years following. Roosting numbers were also tracked monthly from 2018 to 2022 to indicate local population fluctuations in the study area around Hogsback. An average of 112 ± SD 31 Cape Parrots roosted there, with roost counts notably higher from January to June, bolstered by newly-fledged juveniles prior to their dispersal. This study demonstrates the use of flock photographs as an effective, non-invasive tool to assess the demographics and health of an avian population. [ABSTRACT FROM AUTHOR]

While species distribution models (SDM) are frequently used to predict species occurrences to help inform conservation management, there is limited evidence evaluating whether habitat suitability can reliably predict intrinsic growth rates or distinguish source populations from sinks. Filling this knowledge gap is critical for conservation science, as applications of SDMs for management purposes ultimately depend on these typically unobserved population or metapopulation dynamics.Using linear regression, we associated previously published population level estimates of intrinsic growth and abundance derived from a Bayesian analysis of mark‐recapture data for 17 bird species found in the contiguous United States with SDM habitat suitability estimates fitted here to opportunistic data for these same species. We then used the area under the ROC curve (AUC) to measure how well SDMs can distinguish populations categorized as sources and sinks. We built SDMs using two different approaches, boosted regression trees (BRT) and generalized linear models (GLM), and compared their source/sink predictive performance. Each SDM was built with presence points obtained from eBird (a web‐available database) and 10 environmental variables previously selected to model intrinsic growth rates and abundance for these species.We show that SDMs built with opportunistic data are poor predictors of species demography in general; both BRT and GLM explained very little spatial variation of intrinsic growth rate and population abundance (median R2 across 17 species was close to 0.1 for both SDM methods). SDMs, however, estimated higher suitability for source populations as compared to sinks. Out of 13 species which had both source and sink populations, both BRT and GLM had AUC values greater than 0.7 for 7 species when discriminating between sources and sinks.Habitat suitability have the potential to be a useful measure to indicate a population's ability to sustain itself as a source population; however more research on a diverse set of taxa is essential to fully explore this potential. This interpretation of habitat suitability can be particularly useful for conservation practice, and identification of explicit cases of when and how SDMs fail to match population demography can be informative for advancing ecological theory. [ABSTRACT FROM AUTHOR]

Queen parrotfish Scarus vetula and stoplight parrotfish Sparisoma viride are widely distributed throughout the subtropical/tropical regions of the northwestern Atlantic, play important ecological roles in reef ecosystems, and contribute to small-scale commercial landings within several Caribbean management jurisdictions. Prior to this work, no comprehensive life history information existed for either species that combined otolith analysis and gonad histology. Queen parrotfish (n = 390) and stoplight parrotfish (n = 1801) were sampled throughout the U.S. Caribbean from 2013 to 2023. Queen parrotfish range in size from 82 to 402 mm FL and age from 0 to 16 years; stoplight parrotfish ranged from 73 to 433 mm FL and 0 to 20 years. Growth parameter estimates for queen parrotfish were L∞ = 347 mm FL and K = 0.42, when t0 was fixed to −0.06; for stoplight parrotfish, L∞ = 332 mm FL and K = 0.39, with a fixed t0 of −0.06. All female queen parrotfish transitioned to males by a maximum length and age of 322 mm FL and 14 years. In contrast, not all female stoplight parrotfish transitioned to males since the largest and oldest individuals sampled were females. Spawning capable queen parrotfish females were collected from November to August indicating a protracted spawning season of 10 months. Stoplight parrotfish exhibited year-round spawning with >50% of mature females in the spawning capable phase during all months of the year. Based on our overall findings related to life history, queen parrotfish and stoplight parrotfish in the U.S. Caribbean did not appear to exhibit signs of overexploitation which may in part relate to U.S. Caribbean management efforts currently in place that limit the minimum mesh size for traps (which ensures that smaller fish can escape from the traps), a ban on using gillnets to target parrotfish species, and the market driven targeting of "plate-size" fish by commercial spearfishers. The life history information documented in the current study will provide essential information for stock assessments and informed management in the U.S. Caribbean for these two important parrotfish species. [ABSTRACT FROM AUTHOR]

Conservation management and sustainable use of Moringa peregrina are needed to overcome overexploitation coupled with potential environmental changes. This study demonstrates the energy dynamics of M. peregrina, how stored energy influences species persistence amidst environmental challenges, and the importance of energy reserves in the resilience of the species population. Field, greenhouse, and lab experiments were conducted at the levels of population cohorts, plant organs, seeds, and seedlings to demonstrate the relationship between energy content and the persistence of the species. Seedlings and juveniles stored around 12,000 joule/g in roots, while uncoppiced adults stored about 9,000 joule/g in stems, and coppiced adults stored 1,800-4,000 joule/g in lignotubers. In adult trees, the number of sprouting stems is correlated with the energy content in lignotubers. Over the ten years of seed storage, a rapid rate of energy depletion was observed, ranging from 16,821 to 5,059 joule/g, which is associated with decreased germination and viability. The energy content in two-month-old seedlings varied from 240 to 800 joule/seedlings under 200 and 800 mm rainfall, respectively. The unstable population structure could be ascribed to the depletion of stored energy in lignotubers following uncontrolled coppicing and the rapid depletion of seed energy, which hinders the population resilience. [ABSTRACT FROM AUTHOR]

Odontamblyopus sp. is a small burrowing fish widely distributed in coastal waters and intertidal zone of China. Due to the morphological similarity of Odontamblyopus and even Amblyopinae fish, their classification has always been controversial. The lack of genomic information is also not helpful for further analysis of classification and phylogenetics. In this study, we conducted a whole genomic survey of O. sp. based on next-generation sequencing (NGS). A total of 31.30 Gb of high-quality sequence data were obtained in this study. The estimated genome size of O. sp. was 984.05 Mb, with heterozygosity and repetitive sequence rates of 0.66 and 42.94%, and a GC content of approximately 40.23%. The total sequence length of the genome assembly is 920.03 Mb. A total of 227,271 simple sequence repeats (SSRs) were identified, with the highest frequency of repeated motifs being dinucleotide motifs at 58.00%, followed by trinucleotide motifs at 33.00%, tetranucleotide motifs at 7.10%, pentanucleotide motifs at 1.14%, and hexanucleotide motifs at 0.75%. The assembled complete mitochondrial genome sequence was 16,766 bp in length and the structure of its control region were detected and phylogenetic analysis was performed. The results of PSMC (pairwise sequentially Markovian coalescent) analysis showed that two population declines and a population expansion in the Pleistocene, which were consistent with the glacial and interglacial periods, indicating that the population dynamics of O. sp. was closely related to climate conditions. This is the first study on O. sp. genomic characteristics. [ABSTRACT FROM AUTHOR]

Within carnivore guilds, dominant competitors (e.g., lions, Panthera leo) are limited primarily by the density of prey, while subordinate competitors (e.g., African wild dogs, Lycaon pictus) have been limited by the density of dominant competitors. Historically, the fitness and population density of subordinate competitors have not been tightly linked to prey density. However, populations of large herbivores have declined substantially across sub‐Saharan Africa due to human impacts, and where prey depletion is severe, fitness costs for competitive subordinates may begin to outweigh the benefits of competitive release. Using long‐term intensive monitoring of African wild dogs in Zambia's Luangwa Valley Ecosystem (LVE), we tested the effects of prey depletion on survival and reproduction. We hypothesized that African wild dog fitness would be lower in prey‐depleted areas, despite lower lion densities. Our study area included four contiguous regions that varied in protection level, prey density, and lion density. We fit Bayesian Cormack–Jolly–Seber and closed‐capture models to estimate effects on survival and population density, and generalized linear models to estimate effects on reproductive success. We found that the LVE is a stronghold for African wild dogs, with an estimated median density of 4.0 individuals/100 km2. Despite this high density, survival and reproduction differed among regions, and both components of fitness were substantially reduced in the region with the lowest prey density. Anthropogenic prey depletion is becoming an important limiting factor for African wild dogs. If prey depletion (or any other form of habitat degradation) becomes severe enough that its fitness costs outweigh the benefits of competitive release, such changes can fundamentally alter the balance between limiting factors for competitively subordinate species. [ABSTRACT FROM AUTHOR]

In this article, discrete and stochastic changes in (effective) population size are incorporated into the spectral representation of a biallelic diffusion process for drift and small mutation rates. A forward algorithm inspired by Hidden-Markov-Model (HMM) literature is used to compute exact sample allele frequency spectra for three demographic scenarios: single changes in (effective) population size, boom-bust dynamics, and stochastic fluctuations in (effective) population size. An approach for fully agnostic demographic inference from these sample allele spectra is explored, and sufficient statistics for stepwise changes in population size are found. Further, convergence behaviours of the polymorphic sample spectra for population size changes on different time scales are examined and discussed within the context of inference of the effective population size. Joint visual assessment of the sample spectra and the temporal coefficients of the spectral decomposition of the forward diffusion process is found to be important in determining departure from equilibrium. Stochastic changes in (effective) population size are shown to shape sample spectra particularly strongly. • Demography can be modelled via spectral representation of diffusion generators. • Boundary-mutations simplify diffusion models with demography. • Spectral representation of diffusion processes aids assessment of equilibrium. • Short and mild demographic changes affect the shape of sample allele frequencies. • Estimators of past mutation rates can be inferred via sufficient statistics. [ABSTRACT FROM AUTHOR]

The Anastrepha fraterculus complex (AF complex) is a complex of fruit fly species consisting of eight morphotypes distributed across the Americas. In this study, landscape genetics, phylogeographical inferences and coalescence simulations were used to unveil the evolutionary history of the AF complex. Nuclear ribosomal ITS1 sequences from 331 samples distributed in 10 American countries throughout 32 ecoregions and seven biomes were analysed. Results showed high levels of diversity, intraspecific divergence and structuring associated with the different morphotypes of the complex. The analysis of gene flow and genetic diversity showed a clear geographical and environmental pattern. The morphotype–environment association suggested that the cryptic divergence process has involved local adaptation as a mechanism to withstand harsh, novel or variable conditions. The analysis showed a rapid divergence between morphotypes. Haplotypes have been diverging for ~27 000 years before the present, probably enhanced by environmental changes during the Last Glacial Maximum. Diversity estimators and neutrality tests revealed that populations have been experiencing a recent linear growth, starting in the Early Holocene (~11 500 years before the present). The Bayesian phylogeographical and ecological clustering approach detected five spatially separated and ecologically differentiated clusters. Additionally, equatorial Amazonia was indicated to be the most probable ancestral centre of origin for the AF complex. [ABSTRACT FROM AUTHOR]

Community Led Total Sanitation (CLTS) approach was an adopted and piloted environmental intervention done at selected communities in southwest Nigeria. The impact of soil and water bacteria contamination on population demography of select communities with operational CLTS was evaluated. Water (n=64) and soil samples (n=64) collected from communities were estimated for total bacteria (TBC) and coliform counts (TCC). More than 1.50x106 CFU/g TBC were estimated in soil samples and TCC >1.5x106 CFU/g were observed in all the communities. TCC indicated a fecal contamination level of more than 0.50x106 CFU/g (p=0.001). More than 10% occurrence rates of Escherichia coli, Klebsiella oxytoca, Citrobacter species and Pseudomonas aeruginosa were recorded in water and soil samples from all the communities and spore formers (B. megaterium and B. subtilis) ranging from 8.0 to 16.67%. Higher rates of participants (98.0%) resided in these communities with 22.4% and 63.0% were of the age ranges 31-40 and 41 to 50 years respectively. Higher rates of 72.6% were male, predominant occupation were farming (68.5%) and trading (15.4%). Level of education and total number of occupants living in houses were significantly associated with the CLTS (p<0.05). The impact of population demography on the environmental sanitation is yet to improve the sanitation in these communities and CLTS implementation. [ABSTRACT FROM AUTHOR]

We present the first estimate of population dynamics parameters for critically endangered Galápagos pink land iguanas, Conolophus marthae, leveraging mark‐recapture data collected between 2006 and 2021. Demographic parameters were estimated using the POPAN formulation of the Jolly–Seber model. This approach provided a solid and robust estimate, consolidating the results obtained from previous estimates based on the Lincoln–Petersen method evaluating only two sampling occasions. Our results suggest that the abundance of males was higher than that of females at each sampling occasion, probably due to differences in sex‐specific behavior during the reproductive season. Our analyses also provide no evidence of a change in population size during the sampling period, estimated at 150–270 adult individuals, while suggesting positive entry rates. Finally, by comparing the biometric features of first‐captured versus recaptured iguanas, we found that the former have more juvenile‐like characteristics (i.e., they are, on average, smaller) than the latter. Although juvenile pink iguanas have rarely been recorded (only four sampled juvenile‐like individuals in over 16 years of field work), our combined results provide the first clear indication that the only known C. marthae population actively recruits new members from younger age classes. Such recruitment may have prevented any measurable population decline in the last 16 years, but it was also not sufficient to clearly increase the population size. These results are of the utmost importance for the conservation of this species. They will guide future high‐priority actions: (i) aiming at increasing population size by removing or mitigating threats and (ii) increasing the number of individuals by implementing a headstart program and/or founding a second viable population, as identified in the recently published IUCN Conservation and Management Plan. [ABSTRACT FROM AUTHOR]

Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower–Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China. [ABSTRACT FROM AUTHOR]

Species distribution models often suggest strong links between climate and species' distribution boundaries and project large distribution shifts in response to climate change. However, attributing distribution shifts to climate change requires more than correlative models. One idea is to examine correlates of the processes that cause distribution shifts, namely colonization and local extinction, by using dynamic occupancy models. The Cape Rock‐jumper (Chaetops frenatus) has disappeared over most of its distribution where temperatures are the highest. We used dynamic occupancy models to analyse Cape Rock‐jumper distribution with respect to climate (mean temperature and precipitation over the warmest annual quarter), vegetation (proportion of natural vegetation, fynbos) and land‐use type (protected areas). Detection/non‐detection data were collected over two phases of the Southern African Bird Atlas Project (SABAP): 1987–1991 (SABAP1) and 2008–2014 (SABAP2). The model described the contraction of the Cape Rock‐jumper's distribution between SABAP1 and SABAP2 well. Occupancy probability during SABAP1 increased with the proportion of fynbos and protected area per grid cell, and decreased with increases in mean temperature and precipitation over the warmest annual quarter. Mean extinction probability increased with mean temperature and precipitation over the warmest annual quarter, although the associated confidence intervals were wide. Nonetheless, our results showed a clear correlation between climate and the distribution boundaries of the Cape Rock‐jumper, and in particular, the species' aversion for higher temperatures. The data were less conclusive on whether the observed range contraction was linked to climate change or not. Examining the processes underlying distribution shifts requires large datasets and should lead to a better understanding of the drivers of these shifts. [ABSTRACT FROM AUTHOR]

Climate change is a multidimensional phenomenon. As such, no single metric can capture all trajectories of change and associated impacts. While numerous metrics exist to measure climate change, they tend to focus on central tendencies and neglect the multidimensionality of extreme weather events (EWEs). EWEs differ in their frequency, duration, and intensity, and can be described for temperature, precipitation, and wind speed, while considering different thresholds defining “extremeness.” We review existing EWE metrics and outline a framework for classifying and interpreting them in light of their foreseeable impacts on biodiversity. Using an example drawn from the Caribbean and Central America, we show that metrics reflect unequal spatial patterns of exposure across the region. Based on available evidence, we discuss how such patterns relate to threats to biological populations, empirically demonstrating how ecologically informed metrics can help relate EWEs to biological processes such as mangrove recovery. Unveiling the complexity of EWE trajectories affecting biodiversity is only possible through mobilisation of a plethora of climate change metrics. The proposed framework represents a step forward over assessments using single dimensions or averages of highly variable time series. [ABSTRACT FROM AUTHOR]

Climate relicts are of particular importance in evolutionary biology because of the strategies they may adopt for long-term survival despite climatic oscillations. However, because their current distribution is usually restricted and fragmented, many climatic relicts are at risk of extinction. Daphnimorpha (Thymelaeaceae) is a genus endemic to Japan that comprises two species (D. capitellata and D. kudoi) with a disjunct distribution in southern Japan. These two shrub species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphisms obtained from multiplexed inter-simple sequence repeats genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed that these two species may have been isolated since the Tertiary period, supporting their status as climate relicts. In addition, D. kudoi showed clear genetic differentiation between the two mountains where it occurred (Mt. Nagata and Mt. Kuromi), with a decline in the effective population sizes inferred during the last glacial period. In contrast, D. capitellata showed no clear intraspecific genetic structure, and its effective population size was relatively stable. These differences could result in contrasting light tolerance between species. For conservation, we recommend managing these species as three evolutionarily significant units (ESUs): D. capitellata, D. kudoi population on Mt. Nagata, and D. kudoi population on Mt. Kuromi. Considering the limited gene flow among subpopulations and small population census, all ESUs require conservation attention to maintain or increase their effective population sizes. [ABSTRACT FROM AUTHOR]

Abstract Functional traits affect the demographic performance of individuals in their environment, leading to fitness differences that scale up to drive population dynamics and community assembly. Understanding the links between traits and fitness is, therefore, critical for predicting how populations and communities respond to environmental change. However, the net effects of traits on species fitness are largely unknown because we have lacked a framework for estimating fitness across multiple species and environments. We present a modelling framework that integrates trait effects on demographic performance over the life cycles of individuals to estimate the net effect of traits on species fitness. This approach involves (1) modelling trait effects on individual demographic rates (growth, survival and recruitment) as multidimensional performance surfaces that vary with individual size and environment and (2) integrating these effects into a population model to project population growth rates (i.e., fitness) as a function of traits and environment. We illustrate our approach by estimating performance surfaces and fitness landscapes for trees across a temperature gradient in the eastern United States. Functional traits (wood density, specific leaf area and maximum height) interacted with individual size and temperature to influence tree growth, survival and recruitment rates, generating demographic trade‐offs and shaping the contours of fitness landscapes. Tall tree species had high survival, growth and fitness across the temperature gradient. Wood density and specific leaf area had interactive effects on demographic performance, resulting in fitness landscapes with multiple peaks. With this approach it is now possible to empirically estimate the net effect of traits on fitness, leading to an improved understanding of the selective forces that drive community assembly and permitting generalizable predictions of population and community dynamics in changing environments.

The endangered status of the African wild dog (Lycaon pictus) calls for conservation urgency, which requires relevant ecological information targeting population patches. However, current information on wild dogs´ population estimates and ecological traits are still lacking in countries like Angola due to long periods of political unrest and vast areas which are poorly accessible to vehicles. To address this need, we assessed the overall distribution and population status of African wild dogs in Bicuar National Park, southwestern Angola. We also examined the availability of potential prey and sympatric competitors in this woodland habitat. This was achieved through Local Ecological Knowledge using semi-structured interviews to park rangers stationed at all vigilance posts, and complemented with camera trapping. Reported sightings show that wild dogs are distributed throughout Bicuar NP, with group sizes ranging from 2 to 38 individuals, including pups. Our findings confirm the presence of a resident breeding population of wild dogs, with available prey base consisting mostly of small to medium sized prey species such as duiker (Sylvicapra grimmia)/steenbok (Raphicerus campestris) and bush pig (Potamochoerus larvatus). The only large competing carnivores are the spotted hyena (Crocuta crocuta) and leopard (Panthera pardus). Overall, results from this study add to the limited information for this species in Angola, revealing Bicuar NP as a stronghold for the conservation of this endangered canid and highlighting the need for several management actions. Furthermore, local knowledge from park rangers can provide a cost-effective approach to survey elusive species in remote regions, which could be implemented in other areas of Angola where baseline information on wild dogs or other threatened wildlife is urgently needed.

Host plants used by phytophagous insects can have significant consequences on demography parameters, overall lifetime fitness and their subsequent population dynamics. Here, we conduct a comparative demographic study between the specialist Zeugodacus cucumis (French) and generalist Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) to determine whether the host plants used by these fly species play any role in their overall lifetime fitness and explains current host use patterns. These two fly species are pests within the north‐eastern region of Australia and we further aimed to use complete life‐history data to determine the population parameters and models that would help identify the sensitive life‐history stage that could be targeted for effective field management. Eggs collected from laboratory‐reared flies were inoculated into organically grown fruits of both the primary and alternate host plant cultivars of both fly species. The proportion surviving each life stage from egg through to adult and fecundity were monitored for all cohorts from the different plant cultivars. Complete stage‐base life‐tables for cohorts of each fly species developing from each fruit cultivar were constructed, and the key demographic parameters and population models were analysed using PopTools matrix model programme. Our results showed that the host used by each fly species had significant consequences on fly demographic parameters and hence their overall lifetime fitness. The generalist B. tryoni was able to compensate for the fitness loss experienced at the pre‐adult stage by having adults with higher fecundity, but this was not the case for the specialist Z. cucumis. Stage‐base population models revealed that the population growth rate of both species was highly sensitive at the adult reproductive stage, indicating that manipulating probability of survival at this life stage would effectively manage populations of these pest species. This study provides the empirical evidence of undertaking complete life history demography studies of phytophagous insects to accurately understand their lifetime fitness consequences of using a certain host, their observed host use patterns, and overall population dynamics. We suggest that any efforts to manage dacine fruit fly pest population should consider life‐history consequences of host use. [ABSTRACT FROM AUTHOR]

Context: Unsustainable harvesting can threaten wildlife populations and jeopardise the livelihoods of people relying on wildlife resources. Although millions of rainbow mudsnakes (Enhydris enhydris) are harvested from wetland agroecosystems in tropical Asia each year, few detailed studies have been conducted on the biology of this species. Aims: We aimed to address this knowledge gap by examining the reproductive biology and resilience to harvesting of E. enhydris , collecting from agricultural landscapes in West Java, Indonesia. Methods: We measured and examined 1731 specimens that had been collected and killed for skins and meat near the city of Cirebon in West Java. Key results: Most snakes that we examined were adults (94% of females, 88% of males), with females outnumbering males overall (69% female). Sex ratios varied seasonally and among processing facilities. Females attained larger body sizes than males, were more heavy-bodied, and had shorter tails relative to snout–vent length. Reproductive traits varied among months, with two peaks in the incidence of gravid snakes occurring in March and September. Litter sizes averaged 11.2 (range 2–31) and increased with maternal body size. About half of the adult females were reproductive (vitellogenic or gravid) at the time of collection. This proportion increased with maternal body size, such that 60–70% of large females were reproductive at the time of collection, suggesting that some females may produce two litters per year. Conclusions: Rainbow mudsnakes remain exceptionally abundant in West Java, despite significant habitat modification and intensive harvesting. Implications: The ability of this species to exploit anthropogenic subsidies in disturbed agricultural landscapes gives it access to plentiful food, and the resultant early maturation, frequent reproduction, and high fecundity enable it to withstand high levels of commercial offtake. Thousands of rainbow mudsnakes are captured and killed for trade in Indonesia each year, questioning the sustainability of this offtake. We examined the reproductive biology of Enhydris enhydris collected from disturbed landscapes in West Java. Collected snakes are mostly adults, quick to mature, reproduce frequently and have large litters. These traits render this species resilient to intensive harvesting. Photograph by Alamsyah Elang Nusa Herlambang. [ABSTRACT FROM AUTHOR]

Functional traits affect the demographic performance of individuals in their environment, leading to fitness differences that scale up to drive population dynamics and community assembly. Understanding the links between traits and fitness is, therefore, critical for predicting how populations and communities respond to environmental change. However, the net effects of traits on species fitness are largely unknown because we have lacked a framework for estimating fitness across multiple species and environments.We present a modelling framework that integrates trait effects on demographic performance over the life cycles of individuals to estimate the net effect of traits on species fitness. This approach involves (1) modelling trait effects on individual demographic rates (growth, survival and recruitment) as multidimensional performance surfaces that vary with individual size and environment and (2) integrating these effects into a population model to project population growth rates (i.e., fitness) as a function of traits and environment. We illustrate our approach by estimating performance surfaces and fitness landscapes for trees across a temperature gradient in the eastern United States.Functional traits (wood density, specific leaf area and maximum height) interacted with individual size and temperature to influence tree growth, survival and recruitment rates, generating demographic trade‐offs and shaping the contours of fitness landscapes. Tall tree species had high survival, growth and fitness across the temperature gradient. Wood density and specific leaf area had interactive effects on demographic performance, resulting in fitness landscapes with multiple peaks.With this approach it is now possible to empirically estimate the net effect of traits on fitness, leading to an improved understanding of the selective forces that drive community assembly and permitting generalizable predictions of population and community dynamics in changing environments. [ABSTRACT FROM AUTHOR]

Climate change has been shown to have significant negative effects on wildlife populations owing to both gradual shifts in mean climatic conditions and an increased frequency of extreme climatic events. Based on a long-term study spanning 40 years, we explore the demographic effect of the exceptionally hot and dry summer of 2018 on the demography of an isolated adder (Vipera berus) population in southern Sweden. In spring 2019, we observed a dramatic decline in adder relative body mass and a concomitant 50% reduction in population size. Our results strongly suggest that the negative impacts on adder demography were the result of a combination of low prey abundance and adder dehydration caused by the extreme climatic conditions during the previous summer. The study provides an example of the significant negative effects of ongoing climate change on vertebrate populations and emphasizes the importance of long-term studies to document the demographic effects of extreme climatic events. [ABSTRACT FROM AUTHOR]

Invasive species that are closely related to each other may have similar population dynamics and, therefore, be controlled by targeting similar life stages. We studied two invasive knapweed species, spotted knapweed (Centaurea stoebe subsp. micranthos) and the hybrid meadow knapweed complex (Centaurea × moncktonii) in New York, USA, to determine their individual population growth rates (λ) across several sites over three years. Both knapweed species had growth rates that were greater than 1 (spotted knapweed λ ranged from 1.005–1.440; meadow knapweed λ ranged from 1.541–2.408), but there was high variability between years and sites. One study population of meadow knapweed was composed primarily of individuals of black knapweed ancestry (C. nigra), a species that, while introduced, is not invasive. For this population, the projected dynamics were stable (λ approximately 1). Elasticity analysis showed that the flowering-to-flowering stage contributed the most to population growth rate for six of seven sites and three additional transitions were also influential for four of seven sites of spotted and meadow knapweed: the seedling-to-vegetative stage, vegetative-to-flowering stage and flowering-to-seedling stage. We simulated how increasing vital rates would affect population growth and found that both spotted and meadow knapweed followed the same pattern. The vital rate of established seedlings maturing to flowering plants had the greatest effect on population growth, followed by the survival of new and established seedlings. In all cases, the responses were non-linear, with small initial changes having a large effect. Increases in the vital rates of later stages also tended to have a positive effect on growth rate, but the effects were more modest. Although the sensitivity analysis indicated that early vital rates had the largest effect on population growth, targeting these stages is not practical for management. Rather, reducing older life stage survival or delaying maturation of vegetative individuals would be more effective. The similarity between the population dynamics and how each life stage contributes to population growth provides support that protocols developed for one species should be effective for the other species with the caveat that any biological control agent should be directly tested on the target species before being utilised. [ABSTRACT FROM AUTHOR]

Climate and environmental changes affect species' morphology and ecology, with different responses to shifting abiotic and biotic factors observed across species. Here, we tested how the structural body size of the pine marten and its population sex ratio shifted over time alongside climate change. We analysed temporal changes in morphological traits using 11 measurements of pine marten skulls (N = 158) collected between 1903 and 2020 and originating from Poland. We linked them with climatic and primary production variations and assessed demographic shifts by calculating temporal sex ratio changes over 61 years (N = 205). Skull size, as a proxy of body size, increased in response to warmer and less snowy winters. However, changes in primary productivity rapidly shaped postorbital constriction regardless of shifts in body size, potentially demonstrating increased diet diversity in pine marten. Congruent with climate change, the population sex ratio has skewed towards males over time. Our results indicate that climate conditions and primary production affect the structural size of the skull, and we highlight the various potential responses of pine marten morphology and ecology to climate change. Recently, shifting population demographics resulting from these processes may constitute a threat to marten populations. [ABSTRACT FROM AUTHOR]

Monitoring variation in population features such as abundance and density is essential for evaluating and implementing conservation actions. Camera trapping can be important for assessing population status and trends and is increasingly used to generate density estimates through capture–recapture models. Moreover, success in using this technique can vary seasonally given shifting animal distributions and camera encounter rates. Notwithstanding these potential advantages, a gap still exists in our understanding of the performance of such models for estimating density of cryptic Neotropical terrestrial carnivores with low encounter rate probability with cameras. In addition, scanty information is available on how sampling design can affect the accuracy and precision of density estimates for Neotropical carnivores. We evaluate the performance of spatially explicit versus nonspatial capture–mark–recapture models for estimating densities and population size of ocelots (Leopardus pardalis) within an Atlantic Forest fragment in Brazil. We conducted two spatially concurrent surveys, a random camera-trap deployment covering the entire study area and a systematic camera-trap deployment in a small portion of the study area, where trails and unpaved roads were located. We obtained 244 photographs of ocelots in the Rio Doce State Park from April 2016 to November 2017, using 54-double camera stations spaced approximately 1.5 km apart (random placement) totaling 4,320 trap-nights and 15-double camera stations spaced from 0.3–10 km apart (systematic placement) totaling 1,200 trap-nights. Using the random placement design, ocelot density estimates were similar during the dry season, 14.0 individuals/km2 (± 5.6 SE , 6.6–30.0, 95% CI) and 13.78 individuals/km2 (± 4.25 SE, 5.4–22.1, 95% CI) from spatially explicit capture–recapture and nonspatial models, respectively. Using the systematic placement design spatially explicit models had smaller and less precise ocelot density estimates than nonspatial models during the dry season. Ocelot density was 12.4 individuals/100 km2 (± 5.0 SE , 5.8–26.7, 95% CI) and 19.9 individuals/km2 (± 5.2 SE , 9.7–30.1, 95% CI) from spatially explicit and nonspatial models, respectively. During the rainy season, we found the opposite pattern. Using the systematic placement design, spatial-explicit models had higher and less precise estimates than nonspatial models. Ocelot density was 24.6 individuals/100 km2 (± 13.9 SE , 8.7–69.4, 95% CI) and 11.89 individuals/km2 (± 3.93 SE , 4.19–19.59, 95% CI) from spatially explicit and nonspatial models, respectively. During the rainy season, we could not compare models using the random placement design due to limited number of recaptures to run nonspatial models. In addition, a single recapture yielded an imprecise population density estimate using spatial models (high SE and large 95% CIs), thus precluding any comparison between nonspatial and spatially explicit models. We demonstrate relative differences and similarities between the performance of spatially explicit and nonspatial capture–mark–recapture models for estimating density and population size of ocelots and highlight that both types of capture–recapture models differ in their estimation depending on the sampling design. We highlight that performance of camera surveys is contingent on placement design and that researchers need to be strategic in camera distribution according to study objectives and logistics. This point is especially relevant for cryptic or endangered species occurring at low densities and having low detection probability using traditional sampling methods. [ABSTRACT FROM AUTHOR]

Climate change–driven phenological shifts alter the temporal distributions of natural populations and communities, but we have little understanding of how these shifts affect natural populations. Using agent-based models, we show that the interaction of within-population synchrony (individual variation in timing) and timing of interspecific interactions shapes ecological and evolutionary dynamics of populations within a seasonal cycle. Low-synchrony populations had lower survival and biomass but relatively stronger individuals. These effects were surprisingly robust and did not require size-based competitive asymmetries. However, reducing population synchrony could either negatively or positively affect population demography depending on whether the phenology of the focal species was advanced or delayed relative to its competitor. Furthermore, selection for earlier hatching increased when the interspecific competitor arrived earlier and when population synchrony was high. These results emphasize the importance of variation in the phenology of individuals within populations to better understand species interactions and predict ecological and evolutionary outcomes of phenological shifts. [ABSTRACT FROM AUTHOR]

The bullhead Cottus gobio is a small‐sized fish whose range extends over most of the European continent, and it is listed in Annex II of EU "Habitat" Directive for its great conservation interest. In the last decades, bullhead populations suffered local decline. Among the factors that negatively affect bullhead populations, major threats are pollution, habitat deterioration, and the massive introduction of salmonids. This study aims to better understand in which way the presence of the Salmo (trutta) trutta affects Cottus gobio populations. The investigation was carried out in two stretches of a stream located in the Orobic Alps (Italy). The downstream stretch hosts a fish assemblage constituted of both bullhead and brown trout, while in the upstream stretch only bullhead is present. An insurmountable barrier isolates the upstream population of C. gobio from trout, while the environmental conditions of the two stretches proved to be fully comparable. We evaluated population structure, habitat preference, and body shape of bullhead populations in both stretches: the results indicate that the presence of trout decreases the number of bullhead adults, reduces the average adult body size, and induces a bullhead suboptimal habitat occupation. However, both populations of C. gobio showed a well‐structured population and good performance indexes, so trout do not seem to be a threat to the population survival. [ABSTRACT FROM AUTHOR]

Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, HE = 0.0742 ± 0.002). Both FST values (0.1582–0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21–5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.

Assessment of population sex ratios allows managers to forecast recruitment dynamics and loss of genetic diversity in natural populations and is important when the focal population is in low abundance and subject to demographic stochasticity. If levels of natural or artificial selection differ for males and females and levels of mortality likewise vary, lower levels of population recruitment, loss of genetic diversity, and genetic drift can occur. Lake sturgeon (Acipenser fulvescens) are a species of conservation concern, where restoration efforts increasingly rely on hatchery supplementation. Raising larvae to the juvenile stage can increase survival during important early life stages; however, knowledge is lacking concerning effects of artificial rearing environments on differential sex-specific survival before release. We genetically determined the sex of 1459 age-0 lake sturgeon from three cohorts (2016 through 2018) using PCR assays of the ALLWSex2 acipenserid sexing marker. Sexed individuals represented three groups: (1) wild-captured dispersing larvae that died during hatchery rearing, (2) wild-captured dispersing larvae that survived hatchery rearing to release, and (3) wild-captured, wild-raised age-0 individuals. Sex ratios of wild-captured larvae (dead + live) were nearly 50:50 in all years surveyed. We observed slight, but non-significant, directionality in sex ratios in the live and dead hatchery-reared larvae and in wild-captured age-0 individuals. Genetic sexing methods allow for analyses during prolonged pre-reproductive periods and associated variable environmental and demographic circumstances, in situations where physical determination of sex is not possible. [ABSTRACT FROM AUTHOR]

The largest known reef manta ray (Mobula alfredi) population in Africa has been monitored for more than 20 years at several locations on the coast of the Inhambane Province in southern Mozambique. Nonetheless, before this study, little had been reported on the population dynamics of M. alfredi from Závora, a remote bay in the region. Photographic mark‐recapture was used to investigate the size and structure of M. alfredi that aggregate at "Red Sands," a reef cleaning station in Závora Bay. An 11 year photographic data set was used to identify 583 M. alfredi individuals between 2010 and 2021. More than half of M. alfredi individuals were resighted at least once, with most encounters (up to 18 for one individual) occurring during the peak sighting period in July–November each year. An even sex ratio was observed, 44% females and 50% males, with no significant difference in resightings between the sexes. Pollock's robust design population models were used to estimate annual abundance, emigration, annual apparent survival and capture probability at Red Sands from July to November over a 6 year period (2016–2021). Abundance estimates varied year to year, ranging from 35 (95% c.i. [30, 45]) up to 233 (95% c.i. [224, 249]) M. alfredi individuals. Given the seasonal affinity of M. alfredi observed at Red Sands, this study highlights the importance of understanding fine‐scale site use within the larger home range of this population to develop local management strategies. [ABSTRACT FROM AUTHOR]

Recently, true crime podcasting has exploded. These podcasts organizations mobilize resources, compete with other organizations, gain legitimacy, and focus on sustaining foundings and preventing mortalities. This study uses a mixed methods approach to explore this media phenomenon from the perspective of organizational ecology. A demography of true crime podcasts was conducted and population density over time was calculated. Content analysis of news articles mentioning "true crime podcasts" was conducted to understand how journalists from other media organizations act as legitimacy agents to confer public legitimacy on organizations within the population. Explanation of the true crime podcasts' ecosystem is provided, as well as evidence of growing public legitimacy. [ABSTRACT FROM AUTHOR]

Background: Temperature-taking behaviors vary with levels of circulating infectious illness; however, little is known about how these behaviors differ by demographic characteristics. Populations with higher perceived risks of illness are more likely to adopt protective health behaviors. Objective: We investigated differences in temperature-taking frequency and the proportion of readings that were feverish among demographic groups (age, gender, urban/rural status) over influenza offseason; influenza season; and waves 1, 2, and 3 of the COVID-19 pandemic. Methods: Using data from smart thermometers collected from May 1, 2019, to February 28, 2021, across the United States, we calculated the frequency of temperature-taking and the proportion of temperature readings that were feverish. Mixed-effects negative binomial and mixed-effects logistic regression analyses were performed to identify demographic characteristics associated with temperature-taking frequency and the proportion of feverish readings, respectively. Separate models were fit over five study periods: influenza offseason (n=122,480), influenza season (n=174,191), wave 1 of COVID-19 (n=350,385), wave 2 (n=366,489), and wave 3 (n=391,578). Results: Both temperature-taking frequency and the proportion of feverish readings differed by study period (ANOVA P<.001) and were the highest during influenza season. During all periods, children aged 2-5 years and 6-11 years had significantly higher frequencies of temperature-taking than users aged 19-30 years, and children had the highest proportion of feverish readings of all age groups, after adjusting for covariates. During wave 1 of COVID-19, users over the age of 60 years had 1.79 times (95% CI 1.76-1.83) the rate of temperature-taking as users aged 19-30 years and 74% lower odds (95% CI 72%-75%) of a reading being feverish. Across all periods, men had significantly lower temperature-taking frequency and significantly higher odds of having a feverish reading compared to women. Users living in urban areas had significantly higher frequencies of temperature-taking than rural users during all periods, except wave 2 of COVID-19, and urban users had higher odds of a reading being feverish in all study periods except wave 1 of COVID-19. Conclusions: Temperature-taking behavior and the proportion of readings that were feverish are associated with both population disease levels and individual demographic characteristics. Differences in the health behavior of temperature-taking may reflect changes in both perceived and actual illness risk. Specifically, older adults may have experienced an increase in perceived risk during the first three waves of COVID-19, leading to increased rates of temperature monitoring, even when their odds of fever were lower than those of younger adults. Men’s perceived risk of circulating infectious illnesses such as influenza and COVID-19 may be lower than that of women, since men took their temperature less frequently and each temperature had a higher odds of being feverish across all study periods. Infectious disease surveillance should recognize and incorporate how behavior impacts illness monitoring and testing. [ABSTRACT FROM AUTHOR]

The New Guinea Highlands were among the first areas where agricultural societies developed about 9 kya. Even today, the highest human population densities can be found in the tropical highlands, those are the most important shelters for societies in this seriously malaria-affected equatorial area. In this study, the distribution and altitudinal patterns of Plasmodium vivax and Plasmodium falciparum malaria, as well as the potential generation numbers and the annual season lengths of the extrinsic transmission periods of the parasites were modelled for the Last Glacial Maximum, the Mid-Holocene Period, 1960–1990 and 2061–2080 in the Papua New Guinea Highland provinces. It was found that areas influenced by Plasmodium vivax malaria have always been larger than the endemic regions of Plasmodium falciparum. After the Last Glacial Period, the extension of the malaria-free areas decreased dramatically. It could trigger the development of agriculture in the highlands in the early Holocene due to the increasing population concentration in malaria-free areas. These malaria-free regions could be stable in the rest part of the Holocene, which could explain the high human genetic and cultural diversity of the New Guinea Highlands. Future models predict the disruption of this stability and the notable decrease of the malaria-free areas in the highlands, especially in the case of Plasmodium vivax malaria, but the upward move in the Plasmodium falciparum -endemic regions also seems to be notable. These changes can negatively affect the demographic stability and cultural complexity of the traditional highlander communities in Papua New Guinea. [ABSTRACT FROM AUTHOR]

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000–500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (∼10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000–226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice. [ABSTRACT FROM AUTHOR]

The paper examines the spending pattern of Indian states on human priority sectors (HPS) during 2001–2019 particularly stressing on its responsiveness towards the Development Goals and Population Demography. The observed expenditure pattern reveals that among all the major Indian States, Bihar is the most vulnerable state having the lowest spending and lowest growth rate of expenditures. We also find Water Sanitation and Family Welfare to be the most neglected subsectors of HPS as these sectors received only 3% of HPS expenditure on an average. Besides, the pattern also exposes the huge inter– state disparities in HPS expenditure, which is detected to be highest as regard Nutrition and has a rising trend for the Family Welfare component. Moreover, in response to Millennium Development Goals we find there was no significant change in spending pattern, however, we find mixed bearing of population demography on the HPS. For instance, states with a large base of rural population are observed to spend more on the priority sector, but contrary to the expectation, the size of the poor population has no bearing on the states' allocation of resources. The findings of the paper are particularly significant for policy prescriptions to attain the Sustainable Development Goals as it offers sufficient evidence of negligence of timely spending on the HPS in response to the development goals and population composition. So, we find there is a need for introspection on HPS spending and its concurrent evaluation in terms of its allocation criterion and timing of allocation. [ABSTRACT FROM AUTHOR]

Coupled with geological and geographical history, climatic oscillations during the Pleistocene period had remarkable effects on species biodiversity and distribution along the northwestern Pacific. To detect the population structure and demographic history of Odontamblyopus lacepedii, 547-bp fragments of the mitochondrial DNA control region were sequenced. A low level of nucleotide diversity (0.0065 ± 0.0037) and a high level of haplotype diversity (0.98 ± 0.01) was observed. The Maximum Likelihood (ML) and Bayes-ian Inference phylogenetic trees showed no significant genealogical structure corresponding to sampling locations. The results of AMOVA and pairwise Fst values revealed some significant genetic differentiation among populations, and the isolation by distance (IBD) analysis supported that the genetic differentiation was associated with the geographic distances. The demographic history of O. lacepedii examined by neutrality tests, mismatch distribution analysis, and Bayesian Skyline Plots (BSP) analysis suggested a sudden population expansion, and the expansion time was estimated to be around the Pleistocene. We hypothesize that the climate changes during the Pleistocene, ocean currents, and larval dispersal capabilities have played an important role in shaping contemporary phylogeographic pattern and population structure of O. lacepedii. [ABSTRACT FROM AUTHOR]

Species with large local abundances tend to occupy more sites. One of the mechanisms proposed to explain this widely reported inter-specific relationship is a cross-scale hypothesis based on dynamics at the population level. Called the vital rates mechanism; it uses within-population demographic processes of population growth and density dependence to predict when inter-specific abundance–occupancy relationships can arise and when these relationships can weaken and even turn negative. Even though the vital rates mechanism is mathematically simple, its predictions has never been tested directly because of the difficulty estimating the demographic parameters involved. Here, using a recently introduced mark-recapture analysis method, we show that there is no relationship between abundance and occupancy among 17 bird species. Our results are consistent with the predictions of the vital rate mechanism regarding the demographic processes that are expected to weaken this relationship. Specifically, we find that intrinsic growth rate and local abundance are not correlated, and density dependence strength shows considerable variation across species. Variability in density dependence strength is related to variability in species-level local average abundance and intrinsic growth rate; species with lower growth rate have higher abundance and are strongly regulated by density dependent processes, especially acting on survival rates. More generally, our findings support a cross-scale mechanism of macroecological abundance–occupancy relationship emerging from density-dependent dynamics at the population level. [ABSTRACT FROM AUTHOR]

Genetic diversity and population demography of Coreius guichenoti from the middle and lower reaches of the Jinsha River were investigated using mitochondrial DNA Cyt b gene and CO I gene sequences. The results showed that 91 haplotypes were identified from 393 individuals based on concatenated sequences, with relatively high haplotype diversity of (0.936±0.006) and low nucleotide diversity of (0.00489±0.00009). Phylogenetic trees and medianjoining Network based on haplotypes indicate that all haplotypes from the middle and lower reaches of the Jinsha River were mixed with each other according to their geographical distribution, but exhibited three distinct haplotype lineages (Clade 1, Clade 2 and Clade 3). Clade 1 diverged at about 3.66 Ma, while Clade 2 and Clade 3 diverged at about 2.93 Ma. Analysis of molecular variance (AMOVA) showed that the larger genetic variances were within different geographical locations (96.62%) and between different haplotype lineages (81.29%), while the lesser genetic variance were between different geographical locations (3.38%) and within different haplotype lineages (18.71%). Pairwise comparisons of genetic differentiation index (Fst) among different populations ranged from --0.008 to 0.045. Except for the insignificant Fst value between PS and other locations, significant but low Fst were investigated between other two locations (Fst<0.05, P<0.05). In contrary, significant maximum genetic differentiation level was revealed between three haplotype lineages (Fst>0.25, P<0.001). Neutrality test, mismatch distribution and Bayesian Skyline Plot (BSP) all revealed that wild populations of C. guichenoti from the middle and lower reaches of the Jinsha River may have experienced the population expansion event. It may happen at 0.0007-0.0004 Ma during the Holocene small glaciers period. It suggests that the uplift of Qinghai-Tibet Plateau and the evolution of glaciers during Holocene small glaciers period may play important effect on the population demography of C. guichenoti in the Jinsha River. In order to better protect the wild resources of C. guichenoti, it was suggested to pay special attention to the three haplotype lineages of C. guichenoti in the middle and lower reaches of the Jinsha River for guiding its culture production. [ABSTRACT FROM AUTHOR]

The crangonid shrimps Argis hozawai , A. lar and A. toyamaensis , co-distributed in the Sea of Japan, exhibit intriguing differences in geographical and bathymetric distributions and in reproductive biology. Argis hozawai (150–250 m depth) and A. lar (200–300 m) are broadly distributed in the north-western Pacific Ocean and spawn relatively large numbers of small eggs, whereas A. toyamaensis (250–2000 m) is distributed in the Sea of Japan and spawns a small number of large eggs. We examined the relationship between egg size and dispersal patterns in the deep sea by comparing genetic population structures using mitochondrial DNA sequence variation. We found little or no genetic divergence within the Sea of Japan for A. hozawai and A. lar , whereas there was a slight but significantly higher genetic differentiation in A. toyamaensis. This suggests that A. toyamaensis has lower dispersal ability than A. hozawai and A. lar , and therefore might maximize larval survival through larger size at hatching, with either direct or abbreviated larval development, to adapt to the deep-sea environment in the Sea of Japan. We also detected the effects of drastic environmental changes during the Pleistocene glacial periods on their demographic processes in the Sea of Japan. [ABSTRACT FROM AUTHOR]

Aim: Several hypotheses are available to predict change in genetic diversity at expanding peripheral ranges. However, empirical evidence to test predictions of the centre–periphery hypothesis (CPH) at contracting range limits is scarce. To address this issue, we assessed spatial patterns of genetic variation, effective population size, and contemporary and historical gene flow in a widespread, Tertiary relict tree species from subtropical China. Location: Warm‐temperate deciduous forests of subtropical China. Taxon: Emmenopterys henryi (Rubiaceae) Methods: We applied kernel density estimation to determine the centre of the species' geographical range. Using microsatellite markers, we assessed genetic structure and diversity in 36 populations (503 individuals) sampled in the centre and periphery across the species' range. We further examined both historical and contemporary gene flow. Finally, we applied coalescent methods to simulate population demography. Results: In support of CPH predictions, the highest density of E. henryi coincided with the geographical centre of the species' distribution range, and genetic diversity significantly declined with distance from this range centre. Historical migration from the core to the edge was significantly higher than in the opposite direction, whereas contemporary migration followed an opposite pattern. Central and peripheral populations had similar levels of genetic differentiation. Main conclusions: Core‐to‐edge patterns of genetic diversity, but not genetic differentiation, were consistent with the CPH in E. henryi. Also in line with the CPH, historical (but not contemporary) migration from the core to the edge was significantly higher than in the opposite direction. Results suggest that the complex topography in subtropical China and population demographic processes may strongly influence whether CPH predictions are met in different population genetic parameters. [ABSTRACT FROM AUTHOR]

SUMMARY: Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high‐quality, chromosome‐level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest‐quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein‐coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (θ = 2.58e−3; π = 1.94e−3) when compared not only to R. delavayi (θ = 11.61e−3, π = 12.97e−3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high‐quality, chromosome‐level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general. Significance Statement: The high‐quality, chromosome‐level genome and the population genomic analysis of the critically endangered Rhododendron griersonianum provide an invaluable resource for future study as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general. [ABSTRACT FROM AUTHOR]

Abstract Background Current patterns of population genetic variation may have been shaped by long-term evolutionary history and contemporary demographic processes. Understanding the underlying mechanisms that yield those patterns is crucial for informed conservation of endangered species. The critically endangered white-headed langur, Trachypithecus leucocephalus, is endemic to a narrow range in southwest China. This species shows very low genetic diversity in its 2 main relict populations, Fusui and Chongzuo. Whether this has been caused by a short evolutionary history or recent population declines is unknown. Therefore, we investigated the contributions of historical and recent population demographic changes to population genetic diversity by using 15 nuclear microsatellite markers and mitochondrial DNA (mtDNA) control region sequences. Results Using genetic data from 214 individuals we found a total of 9 mtDNA haplotypes in the Fusui population but only 1 haplotype in the Chongzuo population, and we found an overall low genetic diversity (haplotype and nucleotide diversities: h = 0.486 ± 0.036; π = 0.0028 ± 0.0003). The demographic history inferred from mtDNA and microsatellite markers revealed no evidence for historical population size fluctuations or recent population bottlenecks. Simulations of possible population divergence histories inferred by DIYABC analysis supported a recent divergence of the Chongzuo population from the Fusui population and no population bottlenecks. Conclusions Despite severe population declines caused by anthropogenic activities in the last century, the low genetic diversity of the extant white-headed langur populations is most likely primarily due to the species’ shallow evolutionary history and to a recent, local population founder event.

It is becoming routine to obtain data sets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study summary statistics that offer enough compression to be tractable, while preserving a great deal of information. One well-studied summary is the site frequency spectrum-the empirical distribution, across segregating sites, of the sample frequency of the derived allele. However, most previous theoretical work has assumed that each site has experienced at most one mutation event in its genealogical history, which becomes less tenable for very large sample sizes. In this work we obtain, in closed form, the predicted frequency spectrum of a site that has experienced at most two mutation events, under very general assumptions about the distribution of branch lengths in the underlying coalescent tree. Among other applications, we obtain the frequency spectrum of a triallelic site in a model of historically varying population size. We demonstrate the utility of our formulas in two settings: First, we show that triallelic sites are more sensitive to the parameters of a population that has experienced historical growth, suggesting that they will have use if they can be incorporated into demographic inference. Second, we investigate a recently proposed alternative mechanism of mutation in which the two derived alleles of a triallelic site are created simultaneously within a single individual, and we develop a test to determine whether it is responsible for the excess of triallelic sites in the human genome.

Dynamic climatic oscillations during the Pleistocene had profound effects on the distribution of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. Analyses of mtDNA sequences from the cytochrome oxidase I gene (911 bp) for 115 individuals of Odontotaenius disjunctus was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. We inferred three lineages that diverged during the Pleistocene and replace each other geographically across the eastern United States. One of these lineages traverses previously identified genetic barriers for terrestrial animals including the Mississippi and Apalachicola Rivers and the Appalachian Mountains. We observed overlapping ranges between two haplotype groups as well as a region of secondary contact associated with ecological transition zone in northern Florida. The two continental lineages depict a genetic signature of a recent population increase associated with expanding niche envelope, whereas the clade restricted to peninsular Florida shows stable populations in a shrinking niche envelope. Given the lack of ecological separation, overlapping distribution of haplogroups and the presence of secondary contact zones, the taxonomic status of these lineages must await robust testing using multilocus DNA data to assess species boundaries. [ABSTRACT FROM AUTHOR]

Eupatorium heterophyllum, belonging to Eupatorium(Asteraceae), is distributed in the eastern Qinghai-Tibet Plateau and Hengduan mountain, and has relatively high elevation in comparison with those of other species within this genus. A survey of two chloroplast DNA(cpDNA)fragments(ycf6-psbM and rpl32-trnL), and one nuclear DNA fragment ITS(nITS)were carried out to assess the genetic diversity and infer the population demography of E. heterophyllum. The results showed that the haplotype diversity(Hd)of combined cpDNA fragments was 0.656, and the nucleotide diversity(π) was 0.001 61 at the species level. These two index values of ITS were 0.687 and 0.002 35, respectively. All these data showed that E. heterophyllum had relatively low level of genetic diversity. Both cpDNA and ITS data show that the total genetic diversity of E. heterophyllum was higher than the average value of populations, and the genetic variations occurred mainly among populations. Significant genetic differentiation exists among populations(cpDNA: Gst=0.679, Nst=0.655, Fst=0.655; nITS: Gst=0.543, Nst=0.370, Fst=0.584). However, there was no obvious phylogeographical structure occurred in E. heterophyllum (Nst < Gst). Both the pattern of haplotype distribution and Network structure of haplotypes indicated that the southern Hengduan mountian and central Yunnan Province were probably the two refugia for E. heterophyllum during the Quaternary Glaciation period. It is infered that E. heterophyllum has not undergone population expansion after glacial period which was supported by the neutral test and mismatch analysis. [ABSTRACT FROM AUTHOR]

Main conclusion: Moderate levels of genetic diversity and differentiation of Anisoptera costata were determined. A population divergence occurred during Younger Dryas. The anthropogenic disturbance had significantly affected the genetic diversity of the species in low tropical forests. Anisoptera costata Korth, an endangered species, is mainly distributed in the lowland tropical forests of the Southeast region in Vietnam, which has not been explored for genetic diversity and demographic history. In this study, eight polymorphic microsatellite markers were used to analyze 232 wild trees of A. costata at nine different populations, representing the natural distribution range of the species in Vietnam. Genetic diversity within the populations was determined with mean values of 0.284 and 0.327 observed and expected heterozygosity, respectively, while genetic differentiation among populations was found with Weir and Cockerham index of 0.12 and Hedrick index of 1.38. These results indicated that habitat fragmentation by the anthropogenic disturbance may be the major factor for the low heterozygosity values and affected the number of alleles in all the targeted populations of A. costata in lowland tropical forests. Populations in the Central Southeast area had a higher level of genetic diversity than the populations in the Coastal and Western Southeast areas. The analysis of molecular variance showed that high genetic variation existed within populations (86.15%) compared to the variation among populations. A reduction in the population size of A. costata was determined by BOTTLENECK. Different clustering methods (Bayesian analysis, the neighbor-joining tree, and principal coordinate analysis) suggested optimal genetic clusters related to gene flow among different areas. Approximate Bayesian computation suggested that population divergence occurred during Younger Dryas. We also discussed the measures for species conservation based on these results. [ABSTRACT FROM AUTHOR]

Lefua costata is a primary freshwater fish confining to cold areas in north of the Huai River. They are the suited model for zoogeographic studies for their high environmental dependence. Here, based on D-loop mtDNA gene, the genetic diversity and phylogeography of L. costata were analyzed on the basis of 211 specimens from 18 sampling in 9 basins in north-eastern China. 55 haplotypes were identified, high haplotype diversity (h=0.9304) and nucleotide diversity (π=0.0087) were detected. Haplotype diversity and nucleotide diversity of population in Liaodong Peninsula (LD) were the highest (h=0.8920, π=0.0074), and the farther away from the Liaodong Peninsula, the lower haplotype diversity of the population. The analysis of molecular variance (AMOVA), pairwise comparisons of genetic distance (K2P) and genetic differentiation index (FST) among the populations showed that the genetic differentiation between the LD population and other populations were highly significant. Phylogenetic analyses based on ML and BI methods indicated all haplotypes from the 9 basins were not clustered separated but mixed with each other according to the geographical distribution. Network analysis showed that all haplotypes were divided into three branches: LD population was clustered in branch A; Huai-Huang River population (HH) and Hai-Luan River population (HL) were clustered in branch C; branch B contained all geographic populations. Neutral test and mismatch analysis showed that overall L. costata population experienced population expansion. According to the average evolution rate (1.00%Ma) and fossil calibration point, the divergence time of the populations of L. costata was 0.0477--2.3784 Ma. The earliest divergence time between LD population and other populations was about 2.3784 Ma, and it was speculated that the Liaodong Peninsula is one of the origin center of L. costata and little affected by Quaternary glaciation, other population had been experienced multiple gene exchange through the Huangbohai Plain estuary and the Songliao Ancient Great Lake. [ABSTRACT FROM AUTHOR]