Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species.

Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.

Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic.

Since 2020, clade 2.3.4.4b highly pathogenic avian influenza H5N8 and H5N1 viruses have swept through continents, posing serious threats to the world. Through comprehensive analyses of epidemiological, genetic, and bird migration data, we found that the dominant genotype replacement of the H5N8 viruses in 2020 contributed to the H5N1 outbreak in the 2021/2022 wave. The 2020 outbreak of the H5N8 G1 genotype instead of the G0 genotype produced reassortment opportunities and led to the emergence of a new H5N1 virus with G1's HA and MP genes. Despite extensive reassortments in the 2021/2022 wave, the H5N1 virus retained the HA and MP genes, causing a significant outbreak in Europe and North America. Furtherly, through the wild bird migration flyways investigation, we found that the temporal-spatial coincidence between the outbreak of the H5N8 G1 virus and the bird autumn migration may have expanded the H5 viral spread, which may be one of the main drivers of the emergence of the 2020-2022 H5 panzootic.IMPORTANCESince 2020, highly pathogenic avian influenza (HPAI) H5 subtype variants of clade 2.3.4.4b have spread across continents, posing unprecedented threats globally. However, the factors promoting the genesis and spread of H5 HPAI viruses remain unclear. Here, we found that the spatiotemporal genotype replacement of H5N8 HPAI viruses contributed to the emergence of the H5N1 variant that caused the 2021/2022 panzootic, and the viral evolution in poultry of Egypt and surrounding area and autumn bird migration from the Russia-Kazakhstan region to Europe are important drivers of the emergence of the 2020-2022 H5 panzootic. These findings provide important targets for early warning and could help control the current and future HPAI epidemics.

Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.

Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.

Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant.

Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.

Sex differences in immune gene expression in the brain of a small shorebird.

Males and females often exhibit differences in behaviour, life histories, and ecology, many of which are typically reflected in their brains. Neuronal protection and maintenance include complex processes led by the microglia, which also interacts with metabolites such as hormones or immune components. Despite increasing interest in sex-specific brain function in laboratory animals, the significance of sex-specific immune activation in the brain of wild animals along with the variables that could affect it is widely lacking. Here, we use the Kentish plover (Charadrius alexandrinus) to study sex differences in expression of immune genes in the brain of adult males and females, in two wild populations breeding in contrasting habitats: a coastal sea-level population and a high-altitude inland population in China. Our analysis yielded 379 genes associated with immune function. We show a significant male-biased immune gene upregulation. Immune gene expression in the brain did not differ in upregulation between the coastal and inland populations. We discuss the role of dosage compensation in our findings and their evolutionary significance mediated by sex-specific survival and neuronal deterioration. Similar expression profiles in the coastal and inland populations suggest comparable genetic control by the microglia and possible similarities in pathogen pressures between habitats. We call for further studies on gene expression of males and females in wild population to understand the implications of immune function for life-histories and demography in natural systems.

Current breeding distributions and predicted range shifts under climate change in two subspecies of Black-tailed Godwits in Asia.

Habitat loss and shifts associated with climate change threaten global biodiversity, with impacts likely to be most pronounced at high latitudes. With the disappearance of the tundra breeding habitats, migratory shorebirds that breed at these high latitudes are likely to be even more vulnerable to climate change than those in temperate regions. We examined this idea using new distributional information on two subspecies of Black-tailed Godwits Limosa limosa in Asia: the northerly, bog-breeding L. l. bohaii and the more southerly, steppe-breeding L. l. melanuroides. Based on breeding locations of tagged and molecularly assayed birds, we modelled the current breeding distributions of the two subspecies with species distribution models, tested those models for robustness and then used them to predict climatically suitable breeding ranges in 2070 according to bioclimatic variables and different climate change scenarios. Our models were robust and showed that climate change is expected to push bohaii into the northern rim of the Eurasian continent. Melanuroides is also expected to shift northward, stopping in the Yablonovyy and Stanovoy Ranges, and breeding elevation is expected to increase. Climatically suitable breeding habitat ranges would shrink to 16% and 11% of the currently estimated ranges of bohaii and melanuroides, respectively. Overall, this study provides the first predictions for the future distributions of two little-known Black-tailed Godwit subspecies and highlights the importance of factoring in shifts in bird distribution when designing climate-proof conservation strategies.

Unravelling the processes between phenotypic plasticity and population dynamics in migratory birds.

Populations can rapidly respond to environmental change via adaptive phenotypic plasticity, which can also modify interactions between individuals and their environment, affecting population dynamics. Bird migration is a highly plastic resource-tracking tactic in seasonal environments. However, the link between the population dynamics of migratory birds and migration tactic plasticity is not well-understood. The quality of staging habitats affects individuals' migration timing and energy budgets in the course of migration and can consequently affect individuals' breeding and overwintering performance, and impact population dynamics. Given staging habitats being lost in many parts of the world, our goal is to investigate responses of individual migration tactics and population dynamics in the face of loss of staging habitat and to identify the key processes connecting them. We started by constructing and analysing a general full-annual-cycle individual-based model with a stylized migratory population to generate hypotheses on how changes in the size of staging habitat might drive changes in individual stopover duration and population dynamics. Next, through the interrogation of survey data, we tested these hypotheses by analysing population trends and stopover duration of migratory waterbirds experiencing the loss of staging habitat. Our modelling exercise led to us posing the following hypotheses: the loss of staging habitat generates plasticity in migration tactics, with individuals remaining on the staging habitat for longer to obtain food due to a reduction in per capita food availability. The subsequent increasing population density on the staging habitat has knock-on effects on population dynamics in the breeding and overwintering stage. Our empirical results were consistent with the modelling predictions. Our results demonstrate how environmental change that impacts one energetically costly life-history stage in migratory birds can have population dynamic impacts across the entire annual cycle via phenotypic plasticity.

The Value of Contrast-Enhanced Ultrasound in Diagnosing Small Renal Cell Carcinoma Subtypes and Angiomyolipoma.

OBJECTIVES: To retrospectively explore the value of contrast-enhanced ultrasound (CEUS) in differentiating small renal cell carcinomas (RCCs) from angiomyolipomas (AMLs), and distinguishing between clear cell RCC (ccRCC), papillary RCC (pRCC), and chromophobe RCC (chRCC). METHODS: A total of 151 patients with small renal masses (110 ccRCCs, 12 pRCCs, 9 chRCCs, and 20 AMLs) were enrolled between August 2016 and October 2019. RESULTS: There were significant differences in terms of enhancement intensity (EI), enhancement homogeneity, perilesional rim-like enhancement (PRE), wash in, and wash out (WO) between RCC and AML (P = .000, .011, .000, .001, .000, respectively). Although there was no significant difference in EI between pRCC and chRCC (P = .272), EI of ccRCC was higher than that of pRCC (P = .000) and chRCC (P = .010). Multivariate regression analysis showed PRE and fast WO were related to RCC (OR = 18.189, 15.141, respectively). Although there were no significant differences in the sensitivity and area under the curve (AUC) between PRE and fast WO (95.0% vs. 95.0%, P = 1.000 and .880 vs. 0.799, P = .123, respectively), the specificity of PRE in predicting RCC was higher than that of fast WO (80.92% vs. 64.89%, P = .011). The sensitivity, specificity, and AUC of the two characteristics combination for differentiating RCC from AML were 95.0%, 90.8%, and 0.920, respectively, and that of EI for differentiating between ccRCC, pRCC, and chRCC were 81.0%, 78.2%, and 0.796, respectively. CONCLUSIONS: CEUS has value in differentiating small RCCs from AMLs and distinguishing ccRCC, a subtype associated with a greater likelihood of malignant behavior from pRCC and chRCC.

Spatial Ecology of Asian Water Monitors Adjacent to a Sea Turtle Nesting Beach.

Nest predation is the main cause of hatching failure for many turtle populations. For green turtles (Chelonia mydas) nesting at Chagar Hutang in Redang Island, Malaysia, Asian water monitors (Varanus salvator) are a potential nest predator. However, no studies have documented the space use of this species in coastal habitat adjacent to a sea turtle nesting beach to assess its potential impact on turtle nests. Here, we used Global Positioning System (GPS) data loggers to quantify space use of Asian water monitors in order to establish the extent to which they use sea turtle nesting areas. Asian water monitors had a diurnal activity pattern and spent most of their time in rain forest habitat behind the sea turtle nesting beach. The home range occupied by Asian water monitors varied between 0.015 and 0.198 km2 calculated by the Kernel Brownian Bridge method. The space use patterns of individual Asian water monitors varied between individuals. Two males had relatively small home ranges, whereas one male and the female had a relatively large home range. Because tracked Asian water monitors in this study rarely visited the sea turtle nesting areas, it is probable that only a few individuals are responsible for opening nests.

Occurrence and risks of PCDD/Fs and PCBs in three raptors from North China.

Concentrations of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and polychlorinated biphenyls (PCBs) were investigated in muscle samples from common kestrels (Falco tinnunculus), eagle owls (Bubo bubo), and little owls (Athene noctua) collected in Beijing, China. The concentrations of PCDD/Fs were in the ranges of 22.7-5280, 67.5-1610, and 68.4-3180 pg/g lipid weight (lw), while levels of dioxin-like PCBs ranged from 4.91 to 1560, 8.08-294, and 28.2-3540 ng/g lw, in common kestrel, eagle owl, and little owl, respectively. The main PCDD/Fs congener was 2,3,4,7,8-PeCDF, and CB-153 dominated the seven indicator PCBs. PCB levels have shown a decreasing trend in the last decade for the common kestrel, but not for little owl in Beijing, which exhibited higher levels of pollutants and toxic equivalency (TEQ) values than the other two species. Concentrations of PCDD/Fs, dioxin-like PCBs, and indicator PCBs differed between fledgling and adult raptors for certain species. Raptors in this study generally had a higher TEQ than the no-observed-effect level in the literature, indicating significant exposure risks to PCDD/Fs and dioxin-like PCBs in raptors, especially in adult little owls.

Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences.

The advent of the phylogenomic era has significantly improved our understanding of the evolutionary history and biogeography of Southeast Asia's diverse avian fauna. However, the taxonomy and phylogenetic relationships of many Southeast Asian birds remain poorly resolved, especially for those with large geographic ranges, which might have experienced both ancient and recent geological and environmental changes. In this study, we examined the evolutionary history and biogeography of the hill partridges (Galliformes: Phasianidae: Arborophila spp.), currently the second most speciose galliform genus, and thought to have colonized Southeast Asia from Africa. We present a well-resolved phylogeny of 14 Arborophila species inferred from ultra-conserved elements, exons, and mitochondrial genomes from both fresh and museum samples, which representing almost complete coverage of the genus. Our fossil-calibrated divergence time estimates and biogeographic modeling showed the ancestor of Arborophila arrived in Indochina during the early Miocene, but the initial divergence within Arborophila did not occur until ~10 Ma when global cooling intensified. Subsequent dispersal and diversification within Arborophila were driven by several tectonic and climatic events. In particular, we found evidence of rapid radiation in Indochinese Arborophila during the Pliocene global cooling and extensive dispersal and speciation of Sundaic Arborophila during the Pleistocene sea-level fluctuations. Taken together, these results suggest that the evolutionary history and biogeography of Arborophila were influenced by complex interactions among historical, geological and climatic events in Southeast Asia.

Prolactin concentrations predict parental investment and nest survival in a free-living shorebird.

The hormonal milieu that exists during reproduction is one of the key factors influencing the trade-off between reproductive investment and self-maintenance. Much previous work in birds has focused on prolactin as a physiological mediator since prolactin is involved in the onset and maintenance of parental care. However, how prolactin relates to reproductive success in terms of altering parental behavior in wild bird populations is not fully understood. Here, we report prolactin concentrations in breeding Kentish plovers (Charadrius alexandrinus), a small shorebird with variable mating systems and parental care, as an ecological model of mating system evolution. Throughout the breeding season, we estimated the circulating prolactin concentrations in male and female plovers during incubation. In addition, we monitored parental behavior and determined the fate of nests. We found that prolactin concentrations decreased during incubation but increased with clutch completion date. In addition, males and females with high prolactin concentrations spent more time on incubation than those with low prolactin concentrations. Importantly, higher prolactin concentrations in either males or females predict higher nest survival. Our results suggest that prolactin is an indicator of parental behavior in a wild shorebird population, although additional studies including experimental manipulation of prolactin concentrations are necessary to verify this relationship.

The independent indicators for differentiating renal cell carcinoma from renal angiomyolipoma by contrast-enhanced ultrasound.

BACKGROUND: The value of contrast-enhanced ultrasound (CEUS) in differentiating between renal cell carcinoma (RCC) and angiomyolipoma (AML) was analyzed. The purpose of this study was to identify the independent indicators of CEUS for predicting RCC. METHODS: A total of 172 renal tumors (150 RCCs, 22 AMLs) in 165 patients underwent conventional ultrasound (CUS) and CEUS examinations before radical or partial nephrectomy, and the features on CUS and CEUS were analyzed. RESULTS: There were significant differences in echogenicity, blood flow signals in color Doppler flow imaging (CDFI), peak intensity, homogeneity of enhancement, wash in, wash out, and perilesional rim-like enhancement between RCC and AML (P < 0.05 for all). Multivariate analysis indicated that perilesional rim-like enhancement (P = 0.035, odds ratio [OR] = 9.907, 95% confidence interval [CI]: 1.169-83.971) and fast wash out (P = 0.001, OR = 9.755, 95%[CI]: 2.497-38.115) were independent indicators for predicting RCC. The area under the receiver operating characteristic (ROC) curve (AUC) for perilesional rim-like enhancement was 0.838 (95% CI: 0.774-0.890) with 76.7% sensitivity and 90.9% specificity, while the AUC of fast wash out was 0.833 (95% CI:0.768-0.885) with 74.7% sensitivity and 81.8% specificity. CONCLUSIONS: This study indicated that CEUS has value in differentiating RCC and AML. Present perilesional rim-like enhancement and fast wash out may be important indicators for predicting RCC.

Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast.

BACKGROUND: Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient shorebird species, the Kentish (Charadrius alexandrinus) and the White-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. RESULTS: Our integrative analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamic isolation with secondary contact occurring due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. CONCLUSION: These findings imply that ecology can indeed counter gene flow through divergent selection and thus contributes to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and assist the inference of mechanisms of speciation.

A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes.

Next-generation DNA sequencing (NGS) offers a promising way to obtain massive numbers of orthologous loci to understand phylogenetic relationships among organisms. Of particular interest are old museum specimens and other samples with degraded DNA, where traditional sequencing methods have proven to be challenging. Low coverage shotgun sequencing and sequence capture are two widely used NGS approaches for degraded DNA. Sequence capture can yield sequence data for large numbers of orthologous loci, but it can only be used to sequence genomic regions near conserved sequences that can be used as probes. Low coverage shotgun sequencing has the potential to yield different data types throughout the genome. However, many studies using this method have often generated mitochondrial sequences, and few nuclear sequences, suggesting orthologous nuclear sequences are likely harder to recover. To determine the phylogenetic position of the galliform genus Tropicoperdix, whose phylogenetic position is currently uncertain, we explored two strategies to maximize data extraction from low coverage shotgun sequencing from approximately 100-year-old museum specimens from two species of Tropicoperdix. One approach, a simple read mapping strategy, outperformed the other (a reduced complexity assembly approach), and allowed us to obtain a large number of ultraconserved element (UCE) loci, relatively conserved exons, more variable introns, as well as mitochondrial genomes. Additionally, we demonstrated some simple approaches to explore possible artifacts that may result from the use of degraded DNA. Our data placed Tropicoperdix within a clade that includes many taxa characterized with ornamental eyespots (peafowl, argus pheasants, and peacock pheasants), and established relationships among species within the genus. Therefore, our study demonstrated that low coverage shotgun sequencing can easily be leveraged to yield substantial amounts and varying types of data, which opens the door for many research questions that might require information from different data types from museum specimens.

Glaciation-based isolation contributed to speciation in a Palearctic alpine biodiversity hotspot: Evidence from endemic species.

Organisms are unevenly distributed on earth and the evolutionary drivers of that have puzzled ecologists and evolutionary biologists for over a century. Even though many studies have focused on the mechanisms of unevenly distributed fauna and flora, there remains much to learn about the evolutionary drivers behind biodiversity hotspots. In the Tibetan Plateau and Hengduan Mountains, a biodiversity hotspot in the Palearctic realm, alpine uplift cannot be the driver for recent speciation (

The role of niche divergence and geographic arrangement in the speciation of Eared Pheasants (Crossoptilon, Hodgson 1938).

One of the most contentious theories in current ecology is the ecological niche conservatism, which is defined as conservatism among closely related species; however, the ecological niche can also be shifted, as documented in several cases. Genetic drift and ecological divergent selection may cause ecological niche divergence. The current study aims to test whether the ecological niche is conserved or divergent and to determine the main factor that drives ecological niche divergence or conservation. We analyzed the phylogenetic relationship, ecological niche model (ENM) and demographic history of Eared Pheasants in the genus Crossoptilon (Galliformes: Phasianidae) to test niche conservatism with respect to different geographically distributed patterns. The phylogenetic relationship was reconstructed using ∗BEAST with mitochondrial cytochrome b (cyt b) and 44 unlinked autosomal exonic loci, and ENMs were reconstructed in MAXENT using an average of 41 occurrence sites in each species and 22 bioclimatic variables. A background similarity test was used to detect whether the ecological niche is conserved. Demographic history was estimated using the isolation with migration (IM) model. We found that there was asymmetric gene flow between the allopatric sister species Crossoptilon mantchuricum and C. auritum and the parapatric sister species C. harmani and C. crossoptilon. We found that ecological niches were divergent, not conserved, between C. mantchuricum and C. auritum, which began to diverge at approximately 0.3 million years ago. However, the ecological niches were conserved between C. crossoptilon and C. harmani, which gradually diverged approximately half a million years ago. Ecological niches can be either conserved or divergent, and ecological divergent selection for local adaptation is probably an important factor that promotes and maintains niche divergence in the face of gene flow. This study provides a better understanding of the role that divergent selection has in the initial speciation process. The platform combined demographic processes and ecological niches to offer new insights into the mechanism of biogeography patterns.

Community-wide changes in intertaxonomic temporal co-occurrence resulting from phenological shifts.

Global climate change is known to affect the assembly of ecological communities by altering species' spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species' temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here, we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon groups from 329 local meteorological observatories across China. We show that widespread shifts in phenology have resulted in community-wide changes in the temporal overlap between taxa that are dominated by extensions, and that these changes are largely due to taxa's altered span of temporal occurrence rather than the degree of synchrony in phenological shifts. Importantly, our findings also suggest that climate change may have led to less phenological mismatch than generally presumed, and that the context under which to discuss the ecological consequences of phenological shifts should be expanded beyond asynchronous shifts.

Was the exposed continental shelf a long-distance colonization route in the ice age? The Southeast Asia origin of Hainan and Taiwan partridges.

Research on island biotas has greatly contributed to the development of modern evolutionary and biogeographic theories. Until now, most studies have suggested that continental islands received their biotas directly from the adjacent mainland. However, only a few studies have indicated that species on continental islands might originate from other distantly non-adjacent regions. Here, we used the hill partridges (genus Arborophila) that are widely distributed in the southwest and southeast China mainland, Indochina, Hainan and Taiwan islands to test whether species on continental islands might originate from distant regions rather than the adjacent mainland. Based on molecular phylogenies inferred from three mitochondrial fragments and three nuclear introns, together with ancestral area reconstruction, we found that the ancestors of the endemic Hainan and Taiwan partridges (A. ardens and A. crudigularis) likely originated from Indochina, rather than the nearby southeast China mainland. The divergence time estimates demonstrate that their ancestors likely colonized Hainan and Taiwan islands using the long exposed continental shelf between Indochina, Hainan and Taiwan islands during glacial periods, which had not been demonstrated before. Thus, integrating distribution data with phylogenetic information can shed new lights on the historical biogeography of continental islands and surrounding mainland regions.

May brood desertion be ruled by partner parenting capability in a polygamous songbird? An experimental study.

Parents confront multiple aspects of offspring demands and need to coordinate different parental care tasks. Biparental care is considered to evolve under circumstances where one parent is not competent for all tasks and cannot efficiently raise offspring. However, this hypothesis is difficult to test, as uniparental and biparental care rarely coexist. Chinese penduline tits (Remiz consobrinus) provide such a system where both parental care types occur. Here, we experimentally investigated whether parents in biparental nests are less capable of caring than parents in uniparental nests. We monitored parenting efforts at (1) naturally uniparental and biparental nests and (2) biparental nests before and during the temporary removal of a parent. Given the relatively small sample sizes, we have employed various statistical analyses confirming the robustness of our results. We found that total feeding frequency and brooding duration were similar for natural uniparental and biparental nests. Feeding frequency, but not brooding duration, contributed significantly to nestling mass. In line with this, a temporary parental removal revealed that the remaining parents at biparental nests fully compensated for the partner's feeding absence but not for brooding duration. This reflects that the manipulated parents are confronted with a trade-off between feeding and brooding and were selected to invest in the more influential one. However, such a trade-off may not occur in parents of natural uniparental care nests. The different capabilities of a parent independently coordinating feeding and brooding tasks suggest that parents from biparental and uniparental nests were exposed to different resource conditions, thereby foraging efficiency may differ between care types.