Historical Population Dynamics Research Articles

Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives

The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.

Molecular Evolutionary Dynamics of Coxsackievirus A6 Causing Hand, Foot, and Mouth Disease From 2021 to 2023 in China: Genomic Epidemiology Study.

Hand, foot, and mouth disease (HFMD) is a global public health concern, notably within the Asia-Pacific region. Recently, the primary pathogen causing HFMD outbreaks across numerous countries, including China, is coxsackievirus (CV) A6, one of the most prevalent enteroviruses in the world. It is a new variant that has undergone genetic recombination and evolution, which might not only induce modifications in the clinical manifestations of HFMD but also heighten its pathogenicity because of nucleotide mutation accumulation. The study assessed the epidemiological characteristics of HFMD in China and characterized the molecular epidemiology of the major pathogen (CV-A6) causing HFMD. We attempted to establish the association between disease progression and viral genetic evolution through a molecular epidemiological study. Surveillance data from the Chinese Center for Disease Control and Prevention from 2021 to 2023 were used to analyze the epidemiological seasons and peaks of HFMD in Henan, China, and capture the results of HFMD pathogen typing. We analyzed the evolutionary characteristics of all full-length CV-A6 sequences in the NCBI database and the isolated sequences in Henan. To characterize the molecular evolution of CV-A6, time-scaled tree and historical population dynamics regarding CV-A6 sequences were estimated. Additionally, we analyzed the isolated strains for mutated or missing amino acid sites compared to the prototype CV-A6 strain. The 2021-2023 epidemic seasons for HFMD in Henan usually lasted from June to August, with peaks around June and July. The monthly case reporting rate during the peak period ranged from 20.7% (4854/23,440) to 35% (12,135/34,706) of the total annual number of cases. Analysis of the pathogen composition of 2850 laboratory-confirmed cases identified 8 enterovirus serotypes, among which CV-A6 accounted for the highest proportion (652/2850, 22.88%). CV-A6 emerged as the major pathogen for HFMD in 2022 (203/732, 27.73%) and 2023 (262/708, 37.01%). We analyzed all CV-A6 full-length sequences in the NCBI database and the evolutionary features of viruses isolated in Henan. In China, the D3 subtype gradually appeared from 2011, and by 2019, all CV-A6 virus strains belonged to the D3 subtype. The VP1 sequences analyzed in Henan showed that its subtypes were consistent with the national subtypes. Furthermore, we analyzed the molecular evolutionary features of CV-A6 using Bayesian phylogeny and found that the most recent common ancestor of CV-A6 D3 dates back to 2006 in China, earlier than the 2011 HFMD outbreak. Moreover, the strains isolated in 2023 had mutations at several amino acid sites compared to the original strain. The CV-A6 virus may have been introduced and circulating covertly within China prior to the large-scale HFMD outbreak. Our laboratory testing data confirmed the fluctuation and periodic patterns of CV-A6 prevalence. Our study provides valuable insights into understanding the evolutionary dynamics of CV-A6.

Phylogeographic Structure and Population Dynamics of Baoxing Osmanthus (Osmanthus serrulatus), an Endemic Species from the Southwest Sichuan Basin, China.

The mountainous regions of southwest China are recognized as pivotal centers for the origin and evolution of Osmanthus species. Baoxing Osmanthus (Osmanthus serrulatus Rehder), a rare and endemic species known for its spring blooms, is sparsely distributed within the high altitude evergreen broad-leaved forests surrounding the southwestern Sichuan Basin. However, persistent anthropogenic disturbances and habitat fragmentation have precipitated a significant decline in its natural population size, leading to the erosion of genetic resources. To assess the genetic status of O. serrulatus and formulate effective conservation strategies, we conducted sampling across ten wild populations, totaling 148 individuals in their natural habitats. We employed two cpDNA fragments (matK and trnS-trnG) to elucidate the phylogeographic structure and historical population dynamics. The results revealed low species-level genetic diversity, alongside pronounced regional differentiation among populations (FST = 0.812, p < 0.05) and a notable phylogeographic structure (NST = 0.698 > GST = 0.396, p < 0.05). Notably, genetic variation was predominantly observed among populations (81.23%), with no evidence of recent demographic expansion across the O. serrulatus distribution range. Furthermore, divergence dating indicated a timeline of approximately 4.85 Mya, corresponding to the late Miocene to early Pleistocene. This temporal correlation coincided with localized uplift events in the southwestern mountains and heightened Asian monsoons, suggesting pivotal roles for these factors in shaping the current phylogeographic pattern of O. serrulatus. These findings support the effective conservation of O. serrulatus germplasm and offer insights into the impact of Quaternary climate oscillations on companion species within evergreen broad-leaved forests. They also enhance our understanding of the origin and evolution of these forests in the southwestern mountains, aiding biodiversity conservation efforts in the region.

Adaptive divergence, historical population dynamics, and simulation of suitable distributions for Picea Meyeri and P. Mongolica at the whole-genome level

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts.

Climate Change Responses of High-Elevation Polylepis Forests

The high mountain forests on Earth are characterized by sharp environmental heterogeneity, high species endemism, and unique phenotypic adaptations. Yet, global warming is jeopardizing this ecosystem as no other as some forests may have nowhere to go beyond the mountain’s summits. One of the most human-endangered high-elevation ecosystems is the Polylepis forest. Despite its vulnerability, forecasting climate reactions in this distinctive high mountain forest type remains a formidable challenge. Therefore, in this study, we modeled climate change responses of high-elevation allopatric Polylepis sericea and P. quadrijuga (Rosaceae) in the northern Andes. The analysis took into account VIF-prioritized bioclimatic variables for near-to-present and future (2081–2100 MPI-ESM1-2-HR) conditions. Model selection was carried out following the AUC scores of 12 MaxEnt and six machine learning algorithms. Predictive power reached 0.97 for MaxEnt’s model fc.H_rm.1 (H-1). Results indicate a moderate vulnerability of P. sericea, with a 29% loss of area in the trailing edge, due to climate change for the period 2081–2100. On the other hand, P. quadrijuga is likely to experience even larger distribution losses, up to 99%, for the same period. The findings of this study suggest that P. quadrijuga, as compared to P. sericea, exhibits a restricted ability to maintain the corresponding habitat requirements in the face of climatic change. Higher niche specialization of P. quadrijuga in the environmentally heterogeneous Eastern Cordillera contrasts with the more generalist nature of P. sericea in the topographically less complex Central Cordillera. In addition to climate change, this trend may be exacerbated by the detrimental effects of agriculture, mining, and an expanding rural population, which represent significant human-driven pressures yet to be modeled in the northern Andean highlands. Yet, based on previous studies, the historical population dynamics during the past glacial cycles suggests that range shifts could play a more significant role at deeper time scales than previously forecasted in the species’ reaction to climate change. Additionally, Polylepis forests may be able to endure at the current locations via local adaptation and plasticity, major drivers of the phenotypic variation in long-lived trees, counteracting the vulnerability scenario under a niche conservatism hypothesis. Ultimately, the modeling procedure employed in this study provides insights into the potential effects of climate change on Polylepis forests 70 years from now. Oncoming studies may consider alternative responses inherent to the gene pool of the species and the interaction with edaphic and biotic agents. We advocate for the application of comparable estimations in other high-elevation tree communities found at the tree line.

A renewed glance at the Palearctic golden eagle: Genetic variation in space and time.

Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th and 20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re-evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north-south genetic gradient, expressed by the difference between Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.

Evolutionary Diversity of Coxsackievirus A6 Causing Severe Hand, Foot, and Mouth Disease - China, 2012-2023.

Coxsackievirus A6 (CVA6) has emerged as a significant pathogen responsible for severe cases of hand, foot, and mouth disease (HFMD). This study aims to delineate the demographic characteristics and analyze the viral evolution of severe HFMD associated with CVA6, thereby assisting in its surveillance and management. In this investigation, 74 strains of CVA6 were isolated from samples collected from severe HFMD cases between 2012 and 2023. The VP1 gene sequences of CVA6 were amplified and analyzed to assess population historical dynamics and evolutionary characteristics using BEAST, DnaSP6, and PopART. A significant portion (94.4%) of severe CVA6-associated HFMD cases (51 out of 54, with 20 lacking age information) were children under 5 years old. Among the 74 CVA6 strains analyzed, 72 belonged to the D3a sub-genotype, while only two strains were D2 sub-genotype. The average genetic distance between VP1 sequences prior to 2015 was 0.027, which increased to 0.051 when compared to sequences post-2015. Historical population dynamics analysis indicated three significant population expansions of severe CVA6-associated HFMD during 2012-2013, 2013-2014, and 2019-2020, resulting in the formation of 65 distinct haplotypes. Consistent with the MCC tree findings, transitioning between regional haplotypes required multiple base substitutions, showcasing an increase in population diversity during the evolutionary process (from 14 haplotypes in 2013 to 55 haplotypes over the subsequent decade). CVA6, associated with severe HFMD, is evolving and presents a risk of outbreak occurrence. Thus, enhanced surveillance of severe HFMD is imperative.

Characterization of the complete chloroplast genome assembly of Amorphophallus yunnanensis Engler, Pflanzenr (Araceae) from southwestern China

Southwestern China is a biodiversity hotspot due to its diverse topography and environment. Amorphophallus yunnanensis is a species of perennial herb that is mainly distributed throughout southwestern China. The genetic diversity and divergence in this species have not been assessed largely due to a lack of genomic resources. To help with the phylogeographic study, we sequenced and assembled the first complete chloroplast genome sequence of A. yunnanensis. The length of the chloroplast genome was 164,417 bp, with an average GC content of 36% (GenBank accession no. OR400247). The genome possessed a typical quadripartite structure, and the lengths of the large single-copy (LSC), small single-copy (SSC), and two inverted repeat (IR) regions were 92,149 bp, 15,182 bp, 28,543bp, and 28,543bp, respectively. A total of 128 genes were annotated across the genome, including 82 protein-coding genes, 8 rRNAs, and 38 tRNAs. The maximum likelihood (ML) phylogeny confirmed the phylogenetic position of Amorphophallus within Araceae, with the Amorphophallus species forming a single monophyletic clade with a high bootstrap value. The ML tree also indicated that A. yunnanensis was most closely related to A. coaetaneus. This newly sequenced chloroplast genome assembly will aid in future studies of genetic diversity, historical population dynamics, and geographic differentiation patterns of A. yunnanensis.

Biodiversity in the Late Middle Ages: Wild Birds in the Fourteenth-Century County of Holland

This article provides a preliminary overview of the species of wild birds that lived in the fourteenth-century County of Holland, now the Netherlands, on the basis of archaeological and historical sources. It argues that scholars should devote more attention to the Late Middle Ages (1300–1500) as a historical baseline for the study of biodiversity, and demonstrates the value of using medieval financial administration (accounts) as a source for such research. The article identifies 46 species of birds, most of which had substantial socio-economic value (birds of prey, wildfowl, herons and spoonbills). Because some bird populations were actively managed to secure a steady supply, it is possible to gain insight into historical population dynamics. This study can also serve as an example in designing similar research on other species and geographical regions.

Resequencing of white jute (Corchorus capsularis L.) provides insights into genome diversity, population historical dynamics, and improvement

Jute is an important natural fibre crop which provides most of the global bast fibre production annually. However, little progress has been made regarding its genomic diversity, historical population dynamics, origins, and improvement. In this study, we re-sequenced 150 accessions of white jute from 9 countries, further studied the genetic diversity, population dynamics, and improvement, and obtained a total of 3269,808 single nucleotide polymorphisms(SNPs) and 1179,601 insertions/deletions(InDels). Based on these markers, 150 accessions were classified into 2 clades: landraces and modern cultivars. Notably, the modern cultivars were partly classified into two offspring groups: one group developed from “D154,” an important Indian variety, and another from “Xin Xuan 1 hao,” a Chinese cultivar. The genetic diversity (π) was estimated for landrace and cultivars at 0.334 × 10−3 and 0.279 × 10−3, which was considerably lower than that for Corchorus olitorius, suggesting that C. capsularis is subject to a stronger breeding selection during improvement than C. olitorius. A total of 12 candidate genes related to improvement were identified by analyzing π and fixation index(FST). Three of the 12 genes may be involved in the methylation and demethylation processes, which can be integrated into an environmentally sensitive molecular engine that promotes rapid improvement. Analysis of population historical dynamics for C. capsularis showed that the population sizes for landraces and modern cultivars went through 3 bottlenecks. The first bottleneck may be due to climate change whereas the last two may be affected by human activities and war. Our results provide new insights into C. capsularis genome variation, phylogenetic relationships, and improvement, helping understand the genetic basis of crucial agronomic traits and facilitating future molecular breeding for jute.

Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum.

Pleistocene climate cycles are well documented to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; approximately 21 000 years ago) are surmised to have led to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of 19 co-distributed boreal-breeding North American bird species from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to Pleistocene deglaciation earlier than the LGM, whereas genetic diversity was maintained throughout the LGM despite shifts in geographical range. We conclude that glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these species. We did not find a relationship between historic population dynamics and migratory strategy, contributing to growing evidence that major switches in migratory strategy during the LGM are unnecessary to explain contemporary migratory patterns.

Long-term demographic trends and spatio-temporal distribution of past human activity in Central Europe: Comparison of archaeological and palaeoecological proxies

Estimating past population dynamics has become a major research topic for archaeology, which uses several proxies for studying past demography. The Czech Republic represents a unique region with abundant digital archaeological and palynological datasets comprising tens of thousands of records covering the whole Holocene. We used these datasets to quantify long-term demographic trends and to delimit past human activity in space and time. Our results, based on large data from both disciplines, are one of the first quantitative results covering the whole Czech Republic. Through summed probability distributions of radiocarbon dates and spatio-temporal modelling of human activity based on archaeological sites, we identified four major demographic events and processes between 10,000 BCE and 1000 CE – the beginning of the Neolithic at 5400 BCE, the Eneolithic/Bronze Age transition in the 3rd millennium BCE, Bronze Age expansion after 1500 BCE, and mediaeval expansion after 500 CE. We identified two settlement cores in the lowlands, with additional inner and outer peripheries with different demographic histories. Our study clearly shows that prehistoric and early historic population dynamics were not a homogenised process and were regionalized according to local environmental and social conditions. The comparison of archaeological results with pollen-based vegetation proxies also showed regional aspects in human-vegetation interactions. Agro-pastoral communities dwelling in the lowlands mostly influenced the openness of the landscape, used for fields and pastures, whereas contemporary communities with a similar economic mode residing in a different region are more visible in pollen records through species and structural changes in woodlands. The agro-pastoral subsistence strategy did not start everywhere with the onset of the Neolithic: in some regions it failed after several centuries, in others, the foraging lifestyle persisted significantly longer, and farming became a major economic strategy much later. Our study shows that archaeological site-based and 14C-based demographic proxies cannot be utilized for all periods and regions due to several limitations. Only the combination of different quantitative and qualitative archaeological proxies for population does reveal important details.

Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma.

Genome introgression is one of the driving forces that can increase species and genetic diversity and facilitate the adaptive evolution of organisms and biodiversity conservation. However, the genomic introgression and its contribution to biodiversity of macrofungi are still unclear. The genus Ganoderma is a typical macrofungal group that plays crucial roles in forest ecosystem as saprophytic organisms and plant pathogens, and is also involved in human health as medicinal mushrooms. Most public Ganoderma genomes are fragmented, and reference genomes and whole-genome information of diverse germplasm resources for many Ganoderma species are lacking, thus hindering functional and evolutionary genomic investigations among Ganoderma species. In this study, we provide high-quality genomes of 10 Ganoderma species and whole-genome variants data of 224 individuals from various ecoregions, enabling us to infer the phylogeny of Ganoderma species and their historical population dynamics. Based on whole-genome variants, widespread and genome-wide introgression among Ganoderma species is revealed. Genes with significant introgression signals were related to stress response, digestive absorption, and secondary metabolite synthesis, factors that may contribute to environmental adaptation and important biocomponent metabolism. CYP512U6, an essential functional gene in the CYP450 family related to Ganoderma triterpene synthesis, was detected with significant introgression and selection signals combined with Ganoderma metabolomic analysis, indicating that both ancient gene exchange and recent domestication have contributed to the categories and content of secondary metabolites of Ganoderma. The reference genomes, whole-genome variants, and metabolite profiles could serve as abundant and valuable genetic resources for evolution, ecology, and conservation investigations of Ganoderma species and other macrofungi.

Historical population dynamics of the Adélie penguin in response to atmospheric-ocean circulation patterns at Beaufort Island, Ross Sea, Antarctica

Changes in sea ice extent and polynya size and productivity associated with climate conditions in the Ross Sea region have an important role on the ecological responses of Adélie penguins ( Pygoscelis adeliae ). Nevertheless, there have been few studies that elaborate on the effects of atmospheric and oceanic circulation on their populations. Here, we reconstructed the population dynamics of Adélie penguins on Beaufort Island during the past 350 years using various alternative geochemical indices and Generalized Additive Models (GAMs). We explored the effects of atmospheric-ocean circulation patterns, including the El Niño-Southern Oscillation (ENSO), the Southern Annular Mode (SAM), and the Amundsen Sea Low (ASL), on the population ecology of penguins. The results indicated that their population on the island has been growing with fluctuations since ~1650 AD, and there were three significant increases, corresponding to 1650–1750, 1825–1900 and after 1950 AD. It was revealed that climate warming in this region was not a necessary factor for penguin population growth, since their populations maintained an increasing trend during the Little Ice Age (LIA) when relatively colder climate conditions prevailed. The present results indicated that atmospheric-ocean circulation patterns likely impose prominent influences on the historical change of penguin populations on Beaufort Island. • Historical penguin population was reconstructed by Generalized Additive Models. • Sea ice extent, polynya and temperature affect the penguin population directly. • Atmospheric-ocean circulation patterns may play a key role on penguins' ecology. • Warming in the Ross Sea region is not mandatory for larger penguin population.

Population genetic variation and historical dynamics of the natural enemy insect Propylea japonica (Coleoptera: Coccinellidae) in China

Propylea japonica (Coleoptera: Coccinellidae) is a natural enemy insect with a wide range of predation in Chinese mainland and is commonly used in pest management. However, its genetic pattern (i.e., genetic variation, genetic structure, and historical population dynamics) is still unclear, impeding the development of biological control of insect pests. Population genetic research has the potential to optimize strategies at different stages of the biological control processes. This study used 23 nuclear microsatellite sites and mitochondrial COI genes to investigate the population genetics of Propylea japonica based on 462 specimens collected from 30 sampling sites in China. The microsatellite dataset showed a moderate level of genetic diversity, but the mitochondrial genes showed a high level of genetic diversity. Populations from the Yellow River basin were more genetically diverse than those in the Yangtze River basin. Propylea japonica has not yet formed a significant genealogical structure in China, but there was a population structure signal to some extent, which may be caused by frequent gene flow between populations. The species has experienced population expansion after a bottleneck, potentially thanks to the tri-trophic plant–insect–natural enemy relationship. Knowledge of population genetics is of importance in using predators to control pests. Our study complements existing knowledge of an important natural predator in agroecosystems through estimating its genetic diversity and population differentiation and speculating about historical dynamics.

Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus.

Simple SummaryGobies form a group of small fish that are extremely adaptable to their environment. However, genomic resources for Gobiidae species are scarce. In this study, high-throughput sequencing technology was used to generate the whole genome data for the shimofuri goby (Tridentiger bifasciatus). In addition to providing basic genomic information, the mitochondrial whole genome, microsatellite markers, and single-copy homologous genes are also explored. The PSMC model is used to provide the historical population dynamics of the shimofuri goby. The results of this study provide a reference for the assembly of a complete genome map and biological research of the shimofuri goby.The shimofuri goby (Tridentiger bifasciatus) is a small and highly adaptable goby, distributed along the coasts of China, the Sea of Japan, and the west coastal and estuarine areas of the Northwest Pacific. Next-generation sequencing was used to generate genome-wide survey data to provide essential characterization of the shimofuri goby genome and for the further mining of genomic information. The genome size of the shimofuri goby was estimated to be approximately 887.60 Mb through K-mer analysis, with a heterozygosity ratio and repeat sequence ratio of 0.47% and 32.60%, respectively. The assembled genome was used to identify microsatellite motifs (Simple Sequence Repeats, SSRs), extract single-copy homologous genes and assemble the mitochondrial genome. A total of 288,730 SSRs were identified. The most frequent SSRs were dinucleotide repeats (with a frequency of 61.15%), followed by trinucleotide (29.87%), tetranucleotide (6.19%), pentanucleotide (1.13%), and hexanucleotide repeats (1.66%). The results of the phylogenetic analysis based on single-copy homologous genes showed that the shimofuri goby and Rhinogobius similis can be clustered into one branch. The shimofuri goby was originally thought to be the same as the chameleon goby (Tridentiger trigonocephalus) due to their close morphological resemblance. However, a complete mitochondrial genome was assembled and the results of the phylogenetic analysis support the inclusion of the shimofuri goby as a separate species. PSMC analysis indicated that the shimofuri goby experienced a bottleneck event during the Pleistocene Glacial Epoch, in which its population size decreased massively, and then it began to recover gradually after the Last Glacial Maximum. This study provides a reference for the further assembly of the complete genome map of the shimofuri goby, and is a valuable genomic resource for the study of its evolutionary biology.

Molecular Phylogeography and Intraspecific Divergences in Siberian Wildrye (Elymus sibiricus L.) Wild Populations in China, Inferred From Chloroplast DNA Sequence and cpSSR Markers.

A detailed understanding of the distribution and degree of genetic variation within a species is important for determining their evolutionary potential, which in return facilitates the development of efficient conservation strategies aimed at preserving adaptive genetic variation. As an important perennial, cool-season grass in temperate Eurasia, increasing attention has been paid to Siberian wildrye (Elymus sibiricus) due to its excellent ecological utilization value and forage production potential in China, particularly in the Qinghai–Tibet Plateau (QTP) regions. In this study, we applied two chloroplast (cp) genes (matK and rbcL), three cp spacer regions (trnY-GUA∼trnD-GUC, atpH∼atpF, and rps4∼trnT-UGU), and six cpSSR markers to the genetic and phylogenetic analysis of 137 wild E. sibiricus accessions from 23 natural populations that represent the main distribution regions in China. The results show the highest genetic diversity (h = 0.913) and haplotype richness (10 haplotypes) for the QTP population, which indicates QTP as the probable diversity center and geographic origin of E. sibiricus in China. Population divergence was high, indicating a significant phylogeographic structure together with a significantly higher Nst value (Nst > Gst, P < 0.05) at the species level, QTP+XJ (combined populations from QTP and Xinjiang), QTP+NC (combined populations from QTP and North China), and XJ+NC (combined populations from Xinjiang and North China) group levels, respectively. An expansion was revealed in the distributional range of E. sibiricus in China from paleo times up to the recent past, while a dramatic range of contraction was predicted for the near future. The predicted main limiting factor for the further spread of E. sibiricus is an increasing global mean temperature. We recommend that the combination of Es-cpDNA1 and Es-cpDNA3+4+5 can be used as effective markers for phylogenetic analysis and phylogeographical history analysis of E. sibiricus. These findings shed new light on the historical population dynamics of cold-season herbs in the QTP region and the north of China and are of great significance for the future establishment of protection and collection strategies for wild E. sibiricus germplasm.

Phylogeographic structure ofSyntrichia caninervisMitt, a xerophytic moss, highlights the expanded during glacial period

AbstractThe rapid uplift of the Qinghai–Tibet Plateau and its aridification has significantly affected the distribution and community structure of the plants in these regions. However, most of the studies have focussed on vascular plants, and it has been unclear whether bryophytes, which are haploid plants, had similar historical population dynamics to other vascular plants during the dramatic geological and climatic environment changes of the Quaternary. This study used Syntrichia caninervis Mitt as the research object and investigated its genetic variation, differentiation and population dynamic history in China. We genotyped 27 populations throughout the distributional range of S. caninervis using two chloroplast DNA regions and 19 nuclear microsatellite loci and supplemented these data with ecological niche modelling of the potential distribution areas from the last interglacial period. The results showed that genetic data consistently identified three clades: the Qinghai–Tibet Plateau, Pamir Plateau–TienShan and Central Asia. The genetic variation of Syntrichia caninervis mainly occurred within populations and in the populations within a specific region. However, there was a significant gene exchange between the different regions. S. caninervis may have expanded during the glacial period and shrank during the interglacial period. This study provides new evidence for the dynamic population history of drought-tolerant bryophytes in response to severe environmental changes during the Quaternary glacial and interglacial cycles.

Biodiversity in the Late Middle Ages: Wild Birds in the Fourteenth-Century County of Holland

This article provides a preliminary overview of the species of wild birds that lived in the fourteenth-century County of Holland, now the Netherlands, on the basis of archaeological and historical sources. It argues that scholars should devote more attention to the Late Middle Ages (1300–1500) as a historical baseline for the study of biodiversity, and demonstrates the value of using medieval financial administration (accounts) as a source for such research. The article identifies 46 species of birds, most of which had substantial socio-economic value (birds of prey, wildfowl, herons and spoonbills). Because some bird populations were actively managed to secure a steady supply, it is possible to gain insight into historical population dynamics. This study can also serve as an example in designing similar research on other species and geographical regions.

Speciation of a subterranean amphipod on the glacier margins in South Eastern Alps, Europe

AbstractAimClimatic oscillations altered distributions through migration, extinction, adaptation or speciation. Their joint effect has been rarely studied. Here, we tested how Pleistocene climatic oscillations shaped the evolutionary history and distribution of a subterranean amphipod. We tested four predictions for extant populations: (i) populations of good dispersers moving along the ice‐sheet margin should have homogenous genetic structure and broad tolerance to temperatures; (ii) adaptation to local temperatures evolved in poor dispersers with spatially structured populations; (iii) Pleistocene extinctions in the range of historical glaciers should reflect founder effects and high sensitivity to low temperatures; (iv) para‐ or allopatric speciation could unfold through diverse scenarios as a response to local adaptation and constrained dispersal.LocationNorth‐Western part of the Balkan Peninsula, Europe.TaxonNiphargus stygius, Amphipoda, Crustacea.MethodsWe used time‐calibrated multilocus phylogenies and multilocus delimitations to test independently evolving lineages. For each lineage, separately we assessed historical population dynamics and dispersal potential, modelled climatic niches and mapped them onto palaeoclimatic maps. Additionally, we conducted enzymatic and respiratory tests of thermal tolerance, and reconstructed historical distribution range using phylogeographical diffusion analyses.ResultsWe identified four independently evolving tentative species, dated to the Pleistocene, with no evidence of extinction events. Three main lineages are parapatric with few pairwise syntopies and no traces of hybridization. They evolved in allopatry and possibly maintained constant effective population sizes. The lineages are phylogeographically substructured, indicating low recent dispersal. They differ in their climatic niche envelopes and physiological responses to unfavourable temperatures.Main conclusionsWe infer that periodic drops of groundwater in the Pleistocene caused two vicariant events and the onset of two allopatric speciation events, followed by phases of dispersal leading to secondary contact and occasional overlap of ranges. Speciation was seemingly fostered by eco‐physiologically differentiation due to adaptation to local climates.