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The path followed by species in the colonization of remote oceanic islands ultimately depends on their phylogenetic constraints and ecological responses. In this study, we aim to evaluate the relative role of geographical and ecological forces in the origin and evolution of the Madeiran ivy ( Hedera maderensis ), a single-species endemic belonging to the western polyploid clade of Hedera . To determine the phylogenetic placement of H. maderensis within the western polyploid clade, we analyzed 40 populations (92 individuals) using genotyping-by-sequencing and including Hedera helix as outgroup. Climatic niche differences among the study species were evaluated using a database with 867 records representing the entire species ranges. To test species responses to climate, 13 vegetative and reproductive functional traits were examined for 70 populations (335 individuals). Phylogenomic results revealed a nested pattern with H. maderensis embedded within the south-western Iberian H. iberica . Gradual niche differentiation from the coldest and most continental populations of H. iberica to the warm and stable coastal population sister to H. maderensis parallels the geographical pattern observed in the phylogeny. Similarity in functional traits is observed for H. maderensis and H. iberica . The two species show leaves with higher specific leaf area (SLA), lower leaf dry matter content (LDMC) and thickness and fruits with lower pulp fraction than the other western polyploid species H. hibernica . Acquisition of a Macaronesian climatic niche and the associated functional syndrome in mainland European ivies (leaves with high SLA, and low LDMC and thickness, and fruits with less pulp content) was a key step in the colonization of Madeira by the H. iberica / H. maderensis lineage, which points to climatic pre-adaptation as key in the success of island colonization (dispersal and establishment). Once in Madeira, budding speciation was driven by geographical isolation, while ecological processes are regarded as secondary forces with a putative impact in the lack of further in situ diversification.

Background Anthropogenic factors potentially affect observed biogeographical patterns in population genetics, but the effects of ancient human activities on the original patterns created by natural processes are unknown. Sinotaia quadrata, a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear whether S. quadrata in Japan was introduced from China and how different human uses and varying geographic patterns affect the contemporary population genetics between the two regions. Thus, we investigated the demography of S. quadrata and detected its genetic structure in Japan and continental East Asia. Results Sinotaia quadrata populations first naturally migrated from continental East Asia to Japan, which is associated with the ancient period in Japanese geohistory (about 70,000 years ago). They were then artificially introduced in association with agriculture expansion by human movements in two recent periods (about 8,000 and 1,200 years ago). Populations in different parts of Japan have their own sources. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. In the background of the historical migration and introduction, contemporary populations in the two regions show different genetic patterns. Population divergence levels were significantly correlated with geographical patterns in Japan and significantly correlated with human interventions variables in continental East Asia, suggesting that long‐term geographical isolation is likely the major factor that shaped the contemporary population genetics in Japan, while modern human uses are likely the major factor in continental East Asia. Conclusions Our preliminary results show a complex demography and unusual genetic patterns in the contemporary populations for a common freshwater snail and are of significance to determine the historical formation and contemporary patterns of biogeography in Japan and continental East Asia. We document the population history and genetic history of the common freshwater snail Sinotaia quadrata in Japan and continental East Asia. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. Long‐term geographical isolation is likely the major factor that shaped the genetic structure of contemporary populations in Japan, while modern human uses are likely the major factor in continental East Asia.

Geographic isolation is a key factor in shaping the genetic structure of many fish species. Two sympatric species, Culter alburnus and C. mongolicus , are economically important fish that are widely distributed in China and have been recently used as new aquaculture species. We used the mitochondrial DNA control region (CR) as a marker to investigate the genetic structure of the two species. Phylogenetic analysis revealed two major lineages (Lineages I and II) that were highly consistent with geographical patterns for C. alburnus and C. mongolicus . Based on genetic distance, the Zhujiang (Pearl) River Basin (ZRB) populations potentially represented a cryptic subspecies, which might be differentiated as the result of strict geographic isolation, an earlier diverged event, or peripheral areas. Genetic diversity analysis suggested that the Changjiang (Yangtze) River Basin (CRB) populations are located at, or near the core region of their origination, not only due to the larger population size at the CRB, but also their habitat diversity and suitability for its survival, and the genetic diversity differences among basin populations were significant for the two species. Moreover, demographic analysis indicated that the two Culter species and most populations had undergone a period of population expansion during warm interglacial periods. However, the C. alburnus population of Huaihe River Basin (Weishan Lake) exhibited different patterns during the interglacial period, which may due to the latest diverged time of HRB and Weishan Lake located at the permafrost. Notably, the ZRB (in Songtao Reservoir) C. mongolicus population showed no genetic diversity and had a unique haplotype, which could be treated as a special gene pool for species conservation. In summary, geographic isolation is most likely responsible for the two Culter species distribution patterns.

The ‘long tail’ nature of rural special education (RSE) suggests that it simultaneously possesses the private nature of discreteness and the public nature of externalities, which can easily cause provision insufficiency. However, this mismatch may have a dynamic intertemporal correction mechanism impacted by different expenditures of supply sectors (governments and other social sectors). This paper uses different models and data from 30 provinces in China from 2003–2014 to analyze this dynamic correction mechanism. This research finds that different kinds of expenditures from different suppliers have divergent effects on this correction. Capital expenses (especially infrastructure construction) have significantly positive effects on the correction, but administrative expenses have significant dual effects on the correction. These effects may be caused by the various governance efficiencies and motivations of all stakeholders in RSE. This paper concludes that we should pay more attention to the accurate recognition and effective satisfaction of RSE affected by the governance efficiency and motivation of different suppliers to achieve this dynamic correction.

Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.

Aim: We aimed to assess the relative influence of the historical and contemporary processes determining global patterns of current β-diversity. Specifically, we quantified the relative effects of contemporary climate and historical plate tectonics on β-diversity at different phylogenetic scales. Location: Global. Time Period: Contemporaneous. Major taxa studied: Mammals and birds. Methods: We analysed the current β-diversity patterns of birds and mammal assemblages at sequential depths in the phylogeny, that is, from the tips to deeper branches. This was done by slicing bird and mammal phylogenetic trees into 66 time slices of 1 Ma (from 0 to 65 Ma) and recording the branches within each slice. Using global distribution data, we defined the branches' geographical distribution as the union of the corresponding downstream species distributions. For each time slice, we (a) computed pairwise β-diversity across all the grid cells for the whole world and (b) estimated the correlation between this β-diversity matrix and contemporary climatic and geographical distances, and past geological distances, a proxy for plate tectonics. Results: Contemporary climate best explained the β-diversity of shallow branches (i.e., species). For mammals, the geographical isolation of landmasses generated by plate tectonics best explained the β-diversity of deeper branches, whereas the effect of past isolation was weaker for birds. Main conclusions: Our study shows that the relative influence of contemporary climate and plate tectonics on the β-diversity of bird and mammal assemblages varies along the phylogenetic time-scale. Our phylogenetic time-scale approach is general and flexible enough to be applied to a broad spectrum of study systems and spatial scales.

Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1103 genomes of environmental and clinical isolates, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if long-range dispersal has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping, aquatic products trade and increased human migration between continents, are responsible for the change of distribution pattern of this species.

Anatomically modern humans originated in Africa around 200 thousand years ago (ka) 1 – 4 . Although some of the oldest skeletal remains suggest an eastern African origin 2 , southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny 5 , 6 . Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1’2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi–Okavango palaeo-wetland of southern Africa 7 , approximately 200 ka (95% confidence interval, 240–165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast–southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet–dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1’2), as supported by extensive south-coastal archaeological evidence 8 – 10 . Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes. Analyses of mitochondrial genomes from populations in southern Africa provide evidence of a southern African origin of anatomically modern humans and a sustained occupation of the homeland before the first migrations of people appear to be driven by regional climate shifts.

The subtribe Espeletiinae (Asteraceae), endemic to the high-elevations in the Northern Andes, exhibits an exceptional diversity of species, growth-forms, and reproductive strategies. This complex of 140 species includes large trees, dichotomous trees, shrubs and the extraordinary giant caulescent rosettes, considered as a classic example of adaptation in tropical high-elevation ecosystems. The subtribe has also long been recognized as a prominent case of adaptive radiation, but the understanding of its evolution has been hampered by a lack of phylogenetic resolution. Herein, we produce the first fully resolved phylogeny of all morphological groups of Espeletiinae, using whole plastomes and about a million nuclear nucleotides obtained with an original de novo assembly procedure without reference genome, and analyzed with traditional and coalescent-based approaches that consider the possible impact of incomplete lineage sorting and hybridization on phylogenetic inference. We show that the diversification of Espeletiinae started from a rosette ancestor about 2.3 Ma, after the final uplift of the Northern Andes. This was followed by two independent radiations in the Colombian and Venezuelan Andes, with a few trans-cordilleran dispersal events among low-elevation tree lineages but none among high-elevation rosettes. We demonstrate complex scenarios of morphological change in Espeletiinae, usually implying the convergent evolution of growth-forms with frequent loss/gains of various traits. For instance, caulescent rosettes evolved independently in both countries, likely as convergent adaptations to life in tropical high-elevation habitats. Tree growth-forms evolved independently three times from the repeated colonization of lower elevations by high-elevation rosette ancestors. The rate of morphological diversification increased during the early phase of the radiation, after which it decreased steadily towards the present. On the other hand, the rate of species diversification in the best-sampled Venezuelan radiation was on average very high (3.1 spp/My), with significant rate variation among growth-forms (much higher in polycarpic caulescent rosettes). Our results point out a scenario where both adaptive morphological evolution and geographical isolation due to Pleistocene climatic oscillations triggered an exceptionally rapid radiation for a continental plant group.

Habitat loss and fragmentation reduce biodiversity and alter species composition in local communities. β diversity describes the variation in species composition between or among communities in fragmented landscapes and has two components: species turnover and nestedness. In this study, we assessed β diversity of ant assemblages on 24 island fragments in the Thousand Island Lake, China. We constructed a species‐level phylogenetic tree and measured five morphological traits of all ant species captured. We then assessed taxonomic (both incidence‐based and abundance‐weighted), functional and phylogenetic β diversity and partitioned β diversity into turnover and nestedness (as well as the contributions of particular species and particular islands). Finally, we examined the relationships between β diversity and a suite of geographical variables (i.e. difference in island area, difference in isolation and inter‐island distance) using Mantel tests. We found taxonomic and phylogenetic turnover components dominated overall β diversity whereas the functional turnover and nestedness components contributed equally to overall β diversity. Overall β diversity increased with increasing difference in isolation and inter‐island distance; however, only abundance‐weighted overall β diversity decreased with increasing difference in island size. Our results indicate that species that were abundant on large islands were also abundant on small islands. We conclude that the dispersal limitation of ants likely shapes the pattern of β diversity along isolation and inter‐island distance gradients. Additionally, functional redundancy of species (i.e. different species share similar functional roles) could also explain β diversity patterns among fragmented habitat islands. Our results highlight the necessity of incorporating both incidence‐based and abundance‐weighted community data when examining β diversity in fragmented landscapes. By partitioning β diversity into the contributions of particular species and particular fragments, our study implies that small patches can be valuable for maintaining biodiversity among ant communities.