Ancient east-west divergence,recent admixture,and multiple marginal refugia shape genetic structure of a widespread oak species (<Emphasis Type="Italic">Quercus acutissima</Emphasis>) in China

The interactions of major topographic features with climate fluctuations over time are key factors that influence the spatial genetic structure of trees species. As an important characteristic of China’s terrain, the boundary between the mountainous West China and the lowland East China has been found to contribute to the divergence of many species. In this study, we examined whether the stepped geomorphology of China has shaped the genetic structure of Quercus acutissima, a widespread oak species native to East Asia, at a much larger geographic scale. Thirty natural populations of the species were sampled across the entire distribution in China and genotyped using ten nuclear microsatellite markers. To determine the genetic structure and demographic history, we conducted Bayesian cluster analysis and approximate Bayesian computation. A significant east-west divergence was detected at the species level, with western populations presenting much stronger differentiation and lower genetic diversity than eastern populations. The divergence between the groups of Southwest China and East China was estimated to have occurred 3.55–2.37 million years ago (Ma), closely associated with the recent uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes during the late Pliocene to the early Pleistocene. The Central China group may arise from the admixture of these two groups, which was dated to 0.83–0.55 Ma, a period covering several interglacial intervals with unusually warm and wet climate in Central China. The spatial genetic structure of Q. acutissima indicates the possibility of central-marginal dispersal dynamics along latitude and existence of multiple refugia at distribution edges. Our findings highlight that the stepped geomorphology in China and climatic changes since the Pliocene play an important role in shaping the intraspecific genetic structure of widespread species in East Asia.     

Density-dependent habitat selection of corridors in a fragmented landscape

This paper assesses the occurrence of density-dependent habitat selection in an urban fragmented landscape, composed of forest fragments (urban parks) connected by corridors (wooded streets), to test the hypothesis that as population density increased in the parks their suitability decreased and individuals entered alternative habitats, such as wooded streets. Density variation of six species was studied during two consecutive breeding seasons. Vegetation structure in wooded streets was significantly less complex than in urban parks, supporting the view that wooded streets were less suitable for breeding birds. Five species (Coal Tit Parus ater , Spotless Starling Sturnus unicolor , Serin Serinus serinus , Black-billed Magpie Pica pica and Woodpigeon Columba palumbus ) showed density- dependent habitat occupation of wooded streets, while the Common Blackbird Turdus merula did not. As park suitability decreased with rising densities, wooded streets became a profitable alternative in terms of foraging, breeding, or for moving between parks. However, the relationships varied both between and within species in different years. Such differences could have been caused by variable rates of human disturbance, renewal of resources and predation risks in wooded streets. More detailed studies are required to determine how birds perceive and regulate their population dynamics in fragments and associated corridors, particularly for species targeted for management.     

吉林向海自然保护区占用喜鹊巢繁殖的鸟类巢记述

部分鸟类在繁殖过程中,为避免被捕食、减少繁殖投入等而选择占用其他鸟类的巢。2014~2016年每年的4~8月,在吉林向海国家级自然保护区记录到4种占用喜鹊巢进行繁殖的鸟类,其中绿头鸭(Anas platyrhynchos)8巢,纵纹腹小鸮(Athene noctua)4巢,长耳鸮(Aiso otus)5巢,麻雀(Passer montanus)6巢。大部分(82.6%)为利用喜鹊的废弃旧巢,而绿头鸭(1巢)、长耳鸮(2巢)和纵纹腹小鸮(1巢)少数侵占喜鹊当年新建的巢。     

Climate change and breeding parameters of great and blue tits throughout the western Palaearctic

Increasing evidence suggests that climate change has consequences on avian breeding phenology. Here, variations in laying date and clutch size of great tit Parus major and blue tit Parus caeruleus within and between breeding populations through the western Palaearctic are examined in relation to climatic fluctuations, measured by the winter North Atlantic Oscillation (NAO) index. Within and across breeding sites, laying date was related to winter‐NAO index such that great and blue tit females lay earlier after warmer, moister winters (positive values of winter NAO‐index). The present study shows that for most populations there is an advancement of laying date, but the rate of change with respect to NAO significantly differed geographically across the western Palaearctic and did not differ between species. However, clutch size of great and blue tits was not affected by climatic fluctuations, presumably because the whole season is being shifted, but not in relation to food supplies. These combined analyses for the two species controlled for potentially confounding variables such as latitude, longitude, elevation and habitat of each study site.     

Population structure of the wild soybean (Glycine soja) in China: implications from microsatellite analyses

Background and Aims Wild soybean (Glycine soja), a native species of East Asia, is the closest wild relative of the cultivated soybean (G. max) and supplies valuable genetic resources for cultivar breeding. Analyses of the genetic variation and population structure of wild soybean are fundamental for effective conservation studies and utilization of this valuable genetic resource. Methods In this study, 40 wild soybean populations from China were genotyped with 20 microsatellites to investigate the natural population structure and genetic diversity. These results were integrated with previous microsatellite analyses for 231 representative individuals from East Asia to investigate the genetic relationships of wild soybeans from China. Key Results Analysis of molecular variance (AMOVA) revealed that 43·92 % of the molecular variance occurred within populations, although relatively low genetic diversity was detected for natural wild soybean populations. Most of the populations exhibited significant effects of a genetic bottleneck. Principal co-ordinate analysis, construction of a Neighbor-Joining tree and Bayesian clustering indicated two main genotypic clusters of wild soybean from China. The wild soybean populations, which are distributed in north-east and south China, separated by the Huang-Huai Valley, displayed similar genotypes, whereas those populations from the Huang-Huai Valley were different. Conclusions The previously unknown population structure of the natural populations of wild soybean distributed throughout China was determined. Two evolutionarily significant units were defined and further analysed by combining genetic diversity and structure analyses from Chinese populations with representative samples from Eastern Asia. The study suggests that during the glacial period there may have been an expansion route between south-east and north-east China, via the temperate forests in the East China Sea Land Bridge, which resulted in similar genotypes of wild soybean populations from these regions. Genetic diversity and bottleneck analysis supports that both extensive collection of germplasm resources and habitat management strategies should be undertaken for effective conservation studies of these important wild soybean resources.     

The oriental fruitfly Bactrocera dorsalis s.s. in East Asia: disentangling the different forces promoting the invasion and shaping the genetic make-up of populations

The Oriental fruit fly, Bactrocera dorsalis sensu stricto, is one of the most economically destructive pests of fruits and vegetables especially in East Asia. Based on its phytophagous life style, this species dispersed with the diffusion and implementation of agriculture, while globalization allowed it to establish adventive populations in different tropical and subtropical areas of the world. We used nine SSR loci over twelve samples collected across East Asia, i.e. an area that, in relatively few years, has become a theatre of intensive agriculture and a lively fruit trade. Our aim is to disentangle the different forces that have affected the invasion pattern and shaped the genetic make-up of populations of this fruit fly. Our data suggest that the considered samples probably represent well established populations in terms of genetic variability and population structuring. The human influence on the genetic shape of populations and diffusion is evident, but factors such as breeding/habitat size and life history traits of the species may have determined the post introduction phases and expansion. In East Asia the origin of diffusion can most probably be allocated in the oriental coastal provinces of China, from where this fruit fly spread into Southeast Asia. The spread of this species deserves attention for the development and implementation of risk assessment and control measures.     

Diverse processes shape deep phylogeographical divergence in Cobitis sinensis (Teleostei: Cobitidae) in East Asia

Little has been known about the impacts of past vicariance events on the phylogeography and population structure of freshwater fishes in East Asia. The aims of this study are to assess the genetic variability with extensive sampling throughout the range of Chinese spiny loach, Cobitis sinensis, and to infer the genetic structure and evolutionary history of populations. Cobitis sinensis in China may have initiated from two ancestral populations, namely Yangtze and Pearl Rivers, which diverged about 7.24 MYA likely due to drainage systems alteration. In the phylogroup I, a southward dispersal event occurred from East China (Yangtze River) to south ZheMin and Hainan subregions, followed by eastward dispersal from ZheMin to south Taiwan. In the phylogroup II, eastward colonization took place from Pearl River to north Taiwan in the late Pliocene, coupled with loss of genetic diversity in the island populations. This study showed that Cenozoic tectonic movements and climatic and sea‐level fluctuations may have shaped the genetic structure of C. sinensis in concert. Highly diverged mtDNA sequences suggest existence of cryptic species in morphospecies C. sinensis.     

Genetic diversity and population structure of the Black-faced Spoonbill (Platalea minor) among its breeding sites in South Korea: Implication for conservation

The endangered Black-faced Spoonbill Platalea minor has experienced drastic reductions in population size, geographic distribution, and habitat availability throughout East Asia. In the present study, we examined population genetic structure and genetic diversity of Black-faced Spoonbills inhabiting five sites off the west coast of South Korea encompassing a few of its major breeding sites. Ten microsatellite loci and the mitochondrial sequence were used to assess patterns of genetic variation based on 63 individuals. Three ND2 haplotypes were found among 61 individuals; the remaining two were identified as Eurasian Spoonbills, revealing an unexpected hybridization between these two species having different ecological niches in South Korea—the Eurasian Spoonbill overwinters in inland areas, whereas the Black-faced Spoonbill inhabits coastal areas during the summer. Analyses of microsatellite variation revealed no discrete population structure among the five breeding sites but very weak genetic differentiation among geographically distant regions. Assignment tests identified several possible migrants among sites. Our findings suggested that Black-faced Spoonbills from the five breeding sites could be managed as a single population and highlighted the importance of conserving the populations from Maedo, Suhaam, and Namdong reservoir, which are geographically close and have retained high levels of genetic diversity and large populations.     

Synchronic east–west divergence in azure‐winged magpies (Cyanopica cyanus) and magpies (Pica pica)*

Morphometric and genetic analyses were performed to investigate the relationships between populations of the azure‐winged magpie (Cyanopica cyanus). In the morphometric analysis 193 specimens were included representing seven of the nine currently accepted subspecies. Among eight characters analysed, four showed significant differences between samples from Spain and Asia. In contrast, the Asian populations/subspecies are not differentiated morphologically except Cyanopica cyanus japonica. The genetic analysis was based on two mitochondrial sequences (control region, cytochromeb gene). The results are in accordance with the morphometric analysis, showing a clear distinction between birds from the western and eastern distribution ranges. The differentiation of C. c. japonica is not found at the sequence level. Both genetic and morphological data support species status of C. cyanus and Cyanopica cooki. The magpie (Pica pica) was included in the phylogenetic study for comparing intraspecific variation. As in C. cyanus, two clearly separated groups are found, one of them containing the far‐eastern populations (Pica pica jankowskii and Pica pica sericea) and the other the remaining subspecies studied. For both the azure‐winged magpie and the magpie the sequence data imply an east–west differentiation, probably caused by long lasting isolation that may have even started in the Pliocene or repeated expansions/restrictions of distribution ranges during the Pleistocene.     

The roles of climate,geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae)

The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty‐five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype‐based subspecies classification. These lineages diverged 2.32–5.23 million years ago (Ma), a timing that closely aligns with the rapid and drastic uplifting of the Qinghai‐Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia.     

Molecular data and ecological niche modelling reveal the Pleistocene history of a semi‐aquatic bug (Microvelia douglasi douglasi) in East Asia

This study investigated the Pleistocene history of a semi‐aquatic bug, Microvelia douglasi douglasi Scott, 1874 (Hemiptera: Veliidae) in East Asia. We used M. douglasi douglasi as a model species to explore the effects of historical climatic fluctuations on montane semi‐aquatic invertebrate species. Two hypotheses were developed using ecological niche models (ENMs). First, we hypothesized that M. douglasi douglasi persisted in suitable habitats in southern Guizhou, southern Yunnan, Hainan, Taiwan and southeast China during the LIG. After that, the populations expanded (Hypothesis 1). As the spatial prediction in the LGM was significantly larger than in the LIG, we then hypothesized that the population expanded during the LIG to LGM transition (Hypothesis 2). We tested these hypotheses using mitochondrial data (COI+COII) and nuclear data (ITS1 + 5.8S+ITS2). Young lineages, relatively deep splits, lineage differentiation among mountain ranges in central, south and southwest China and high genetic diversities were observed in these suitable habitats. Evidence of mismatch distributions and neutrality tests indicate that a population expansion occurred in the late Pleistocene. The Bayesian skyline plot (BSP) revealed an unusual population expansion that likely happened during the cooling transition between LIG and LGM. The results of genetic data were mostly consistent with the spatial predictions from ENM, a finding that can profoundly improve phylogeographic research. The ecological requirements of M. douglasi douglasi, together with the geographical heterogeneity and climatic fluctuations of Pleistocene in East Asia, could have shaped this unusual demographic history. Our study contributes to our knowledge of semi‐aquatic bug/invertebrate responses to Pleistocene climatic fluctuations in East Asia.     

The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard

Ancient climatic fluctuations have caused changes in the demography and distribution of many species. The genetic differentiation between populations of the same species and of sister species is often attributed largely to the more recent Pleistocene fluctuations. Recent interpretations, which implicate earlier episodes, have proved controversial. We address the timing of genetic divergence in the Iberian lizard Lacerta schreiberi by studying the phylogeography of the cytochrome b sequence. The species has a remarkable morphological uniformity, yet our evidence suggests that earlier events in the Pliocene initiated the main divergence between populations. This interpretation implies that the different populations survived through the Pleistocene in separate localities. This conclusion is robust to different molecular clock calibrations. The persistence of earlier differentiation through the Pleistocene has wide implications for our understanding of Pleistocene refugia in this species and, by extension, to the biogeography of the whole region.     

Separated by sand, fused by dropping water: habitat barriers and fluctuating water levels steer the evolution of rock-dwelling cichlid populations in Lake Tanganyika

The conditions of phenotypic and genetic population differentiation allow inferences about the evolution, preservation and loss of biological diversity. In Lake Tanganyika, water level fluctuations are assumed to have had a major impact on the evolution of stenotopic littoral species, though this hypothesis has not been specifically examined so far. The present study investigates whether subtly differentiated colour patterns of adjacent Tropheus moorii populations are maintained in isolation or in the face of continuous gene flow, and whether the presumed influence of water level fluctuations on lacustrine cichlids can be demonstrated in the small-scale population structure of the strictly stenotopic, littoral Tropheus. Distinct population differentiation was found even across short geographic distances and minor habitat barriers. Population splitting chronology and demographic histories comply with our expectation of old and rather stable populations on steeper sloping shore, and more recently established populations in a shallower region. Moreover, population expansions seem to coincide with lake level rises in the wake of Late Pleistocene megadroughts ~100 KYA. The imprint of hydrologic events on current population structure in the absence of ongoing gene flow suggests that phenotypic differentiation among proximate Tropheus populations evolves and persists in genetic isolation. Sporadic gene flow is effected by lake level fluctuations following climate changes and controlled by the persistence of habitat barriers during lake level changes. Since similar demographic patterns were previously reported for Lake Malawi cichlids, our data furthermore strengthen the hypothesis that major climatic events synchronized facets of cichlid evolution across the East African Great Lakes.     

Climatic niche and neutral genetic diversity of the six Iberian pine species: a retrospective and prospective view

Quaternary climatic fluctuations have left contrasting historical footprints on the neutral genetic diversity patterns of existing populations of different tree species. We should expect the demography, and consequently the neutral genetic structure, of taxa less tolerant to particular climatic extremes to be more sensitive to long‐term climate fluctuations. We explore this hypothesis here by sampling all six pine species found in the Iberian Peninsula (2464 individuals, 105 populations), using a common set of chloroplast microsatellite markers, and by looking at the association between neutral genetic diversity and species‐specific climatic requirements. We found large variation in neutral genetic diversity and structure among Iberian pines, with cold‐enduring mountain species (Pinus uncinata, P. sylvestris and P. nigra) showing substantially greater diversity than thermophilous taxa (P. pinea and P. halepensis). Within species, we observed a significant positive correlation between population genetic diversity and summer precipitation for some of the mountain pines. The observed pattern is consistent with the hypotheses that: (i) more thermophilous species have been subjected to stronger demographic fluctuations in the past, as a consequence of their maladaptation to recurrent glacial cold stages; and (ii) altitudinal migrations have allowed the maintenance of large effective population sizes and genetic variation in cold‐tolerant species, especially in more humid regions. In the light of these results and hypotheses, we discuss some potential genetic consequences of impending climate change.     

Habitat-specific effects of a food supplementation experiment on immunocompetence in Eurasian Magpie Pica pica nestlings

Parasite pressure and nutrition are two of the most important factors affecting the trade-off between nestling growth and immune development. During development, energy and nutrients are often limited, and nestlings should only dedicate differentially more valuable resources to their immune system when the associated benefits are high (i.e. in situations of an increased risk of parasitism). In this study, we manipulated nutritional condition of Eurasian Magpie Pica pica nestlings by providing a food supplement. Additionally, the study area was subdivided into two categories of habitat (irrigated and arid) based on the presence of irrigation canals. Nestling diet composition was more varied in the irrigated compared with in the arid habitat. In addition, nestlings of the irrigated habitat showed a significantly higher infestation of both ectoparasites and blood parasites and a significantly higher cell-mediated immunity, but lower tarsus length compared with nestlings of the arid habitat. Food supplementation to nestlings did not affect tarsus length, but increased nestling cell-mediated immunity in the arid habitat only. Based on the recent demonstrated trade-off between growth and immunocompetence in nestlings, we suggest that differences between habitats in nestling diet and parasite prevalence may have caused different priority rules in the allocation of resources between both fitness traits.     

A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene

The impact of quaternary glaciation in eastern China on local fanua and flora has been a topic of considerable interest. We used mitochondrial DNA (mtDNA) sequence data and coalescent simulations to test two general biogeographic hypothesis related to the effects of Pleistocene climatic fluctuations for a widespread ophidian species (Gloydius brevicaudus) in eastern China and Korean Peninsula. The phylogenetic analysis revealed three major lineages, the southeast Coastal, Yangtze and North Lineages. The latter two are closely related and jointly form a continental lineage. Divergence dating and coalescent simulations indicate a Late Pliocene to Early Pleistocene divergence between lineages from the southeast coast and continental interior, followed by a mid-to-late Pleistocene divergence between lineages from the north and the middle-lower Yangtze Valley across East China, suggesting that all these lineages predated the last glacial maximum. An overlapping range between the two lineages within the continental lineage and a secondary contact associated with ecological transition zones on the margins of the North China Plain were also observed. These results show that vicariance patterns dominated the history of G. brevicaudus. Though the climatic events of the Pleistocene have had a marked effect on the historical distribution and intra-specific divergence of reptiles in China, coalescent and non-coalescent demographic analyses indicate that all lineages of G. brevicaudus seem not to have been adversely affected by glacial cycles during the Late Pleistocene, presumably because of an increase in the amount of climatically mild habitat in East Asia due to a decline in elevation and the development of monsoons since the Mid-End Pleistocene.     

Variation in migratory behavior influences regional genetic diversity and structure among American Kestrel populations (Falco sparverius) in North America

Birds employ numerous strategies to cope with seasonal fluctuations in high-quality habitat availability. Long distance migration is a common tactic; however, partial migration is especially common among broadly distributed species. Under partial migration systems, a portion of a species migrates, whereas the remainder inhabits breeding grounds year round. In this study, we identified effects of migratory behavior variation on genetic structure and diversity of American Kestrels (Falco sparverius), a widespread partial migrant in North America. American Kestrels generally migrate; however, a resident group inhabits the southeastern United States year round. The southeastern group is designated as a separate subspecies (F. s. paulus) from the migratory group (F. s. sparverius). Using mitochondrial DNA and microsatellites from 183 and 211 individuals, respectively, we illustrate that genetic structure is stronger among nonmigratory populations, with differentiation measures ranging from 0.060 to 0.189 depending on genetic marker and analysis approach. In contrast, measures from western North American populations ranged from 0 to 0.032. These findings suggest that seasonal migratory behavior is also associated with natal and breeding dispersal tendencies. We likewise detected significantly lower genetic diversity within nonmigratory populations, reflecting the greater influence of genetic drift in small populations. We identified the signal of population expansion among nonmigratory populations, consistent with the recent establishment of higher latitude breeding locations following Pleistocene glacial retreat. Differentiation of F. s. paulus and F. s. sparverius reflected subtle differences in allele frequencies. Because migratory behavior can evolve quickly, our analyses suggest recent origins of migratory American Kestrel populations in North America.     

A SOCIO-ECOLOGY OF MAGPIES PICA PICA

The behaviour and ecology of unmarked Magpies Pica pica living in the Cotswolds were investigated over 18 months. The spacing of nests was significantly more regular than random and breeding pairs defended territories throughout the year. In winter pairs occasionally left territories to feed with non-breeding birds which flocked throughout the year.
Magpies in flocks had a higher averiage feeding rate than birds alone or in pairs. Aggression rates in flocks increased as birds fed closer together and as food patches became richer.
Agonistic interactions between Crows Corvus corone and Magpies were common; Crows frequently dominated Magpies in disputes over food, and Crows also ate Magpie eggs and young. Single Magpies were most often chased by Crows while Magpies in flocks were able to feed longer in the presence of Crows.
Differences in fledgling success among breeding pairs were related to the location of nests; Magpie pairs breeding near Crow nests suffered higher rates of agonistic encounters with Crows and also produced fewer fledglings than did Magpies breeding at greater distances from Crow nests. Magpie nests were located nearer human habitations than were Crow nests.     

Comparative phylogeography of eastern chipmunks and white-footed mice in relation to the individualistic nature of species

Palaeoecological studies have demonstrated that ecological communities as a whole did not remain stable throughout the climatic fluctuations of the Quaternary. The result is that long-term associations of species cannot be inferred by contemporary associations in ecological communities. Therefore, the evolutionary significance of any contemporary ecological interactions among species and of the biotic community within which species have evolved also cannot be assumed from contemporary conditions. Comparative phylogeographic data provide a method to identify species within ecological communities that have shared biogeographic histories. We present an example of a long-term association between populations of two mammalian species, eastern chipmunks (Tamias striatus) and white-footed mice (Peromyscus leucopus), which are commonly associated with deciduous forest habitats. The distribution of mitochondrial DNA variation in T. striatus and P. leucopus from previously glaciated regions of the eastern United States support the hypothesis that, in at least part of their range, genetic lineages of the two species have expanded from similar population sources since the Last Glacial Maximum. In addition, the spatial concordance of genetic lineages of T. striatus and P. leucopus with the oak-savannah forest formations of Wisconsin and Illinois, suggest that populations associated with this community colonized the area in association with a set of arboreal species that comprise their deciduous forest habitat.