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The Eurasian Spoonbill (Platalea leucorodia) and the White Stork (Ciconia ciconia) are emblematic birds of high conservation interest. This article examines their range history in Europe since the end of the last Glacial by analyzing subfossil bone finds of both species, mostly from archaeological excavations. It is shown that two thousand years ago, White Storks occurred exclusively in the territory of the Roman Empire, i.e. the northern border of their distribution ran along the Rhine and Danube rivers. The north-east part of the continent, with its high population density today, was only colonized in the last few centuries. The Spoonbill's patchy occurrence in Europe today appears to be a typical distribution pattern for this species. The subfossil findings also do not indicate a large, closed distribution area for any phase of the last 10,000 years. Some of its distribution islands (e.g. those in the Netherlands) have existed for thousands of years. [ABSTRACT FROM AUTHOR]

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part of the taxonomically challenging genus Desmidorchis, are well‐known for their ecological resilience and medicinal significance. This study sequences the first complete chloroplast genomes of these species, shedding light on their genomic characteristics and evolutionary relationships. The circular genomes of D. penicillata (161 776 bp) and D. retrospiciens (162 277 bp) display a quadripartite structure typical of Angiosperms. Gene content, order, and GC content are consistent, featuring 114 unique genes, including 80 protein‐coding, 30 transfer RNAs, and four ribosomal RNAs genes. Codon usage analysis underscores A/U‐rich preferences, while RNA editing sites, predominantly in ndhB and ndhD genes, suggest post‐transcriptional modifications. Analysis of long repeated sequences reveals a predominance of forward and palindromic repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are abundant, with high presence of mononucleotide, offering potential molecular markers. Comparative analysis with their relatives in subtribe Stapeliinae identifies mutational hotspots such as ycf1, ndhF, trnG(GCC)‐trnfM(CGA) and ndhG‐ndhI that could be potential DNA barcoding markers. The inverted repeat (IR) boundaries analysis revealed an expansion of IR on the small single copy region, leading to the formation of a pseudogene. Overall, substitution rate analysis indicated purifying selection, with a few genes (rpl22, clpP and rps11) showing signatures of positive selection. Additionally, the phylogenetic analysis positioned Desmidorchis within the Stapeliinae clade and strongly supported the sister relationship between D. penicillata and D. retrospiciens. This study provides comprehensive molecular data for future research in Desmidorchis. [ABSTRACT FROM AUTHOR]

Background: The frequent communication between African and Southeast Asian (SEA) countries has led to the risk of imported malaria cases in the China-Myanmar border (CMB) region. Therefore, tracing the origins of new malaria infections is important in the maintenance of malaria-free zones in this border region. A new genotyping tool based on a robust mitochondrial (mt) /apicoplast (apico) barcode was developed to estimate genetic diversity and infer the evolutionary history of Plasmodium falciparum across the major distribution ranges. However, the mt/apico genomes of P. falciparum isolates from the CMB region to date are poorly characterized, even though this region is highly endemic to P. falciparum malaria. Methods: We have sequenced the whole mt/apico genome of 34 CMB field isolates and utilized a published data set of 147 mt/apico genome sequences to present global genetic diversity and to revisit the evolutionary history of the CMB P. falciparum. Results: Genetic differentiation based on mt/apico genome of P. falciparum revealed that the CMB (Lazan, Myanmar) isolates presented high genetic diversity with several characteristics of ancestral populations and shared many of the genetic features with West Thailand (Mae Sot; WTH) and to some extent West African (Banjul, Gambia; Navrongo, Ghana; WAF) isolates. The reconstructed haplotype network displayed that the CMB and WTH P. falciparum isolates have the highest representation (five) in the five ancestral (central) haplotypes (H1, H2, H4, H7, and H8), which are comparatively older than isolates from other SEA populations as well as the WAF populations. In addition, the highest estimate of the time to the Most Recent Common Ancestor (TMRCA) of 42,400 (95% CI 18,300–82100) years ago was presented by the CMB P. falciparum compared to the other regional populations. The statistically significant negative values of Fu's Fs with unimodal distribution in pairwise mismatch distribution curves indicate past demographic expansions in CMB P. falciparum with slow population expansion between approximately 12,500–20,000 ybp. Conclusions: The results on the complete mt/apico genome sequence analysis of the CMB P. falciparum indicated high genetic diversity with ancient population expansion and TMRCA, and it seems probable that P. falciparum might have existed in CMB, WTH, and WAF for a long time before being introduced into other Southeast Asian countries or regions. To reduce the impact of sample size or geographic bias on the estimate of the evolutionary timeline, future studies need to expand the range of sample collection and ensure the representativeness of samples across geographic distributions. Additionally, by mapping global patterns of mt/apico genome polymorphism, we will gain valuable insights into the evolutionary history of P. falciparum and optimised strategies for controlling P. falciparum malaria at international borders. [ABSTRACT FROM AUTHOR]

Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long‐snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine‐lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome‐level genome assembly and described genome‐wide patterns of diversity and divergence through the analysis of 112 whole‐genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked‐read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo‐overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation. [ABSTRACT FROM AUTHOR]

The family Ptychadenidae contains three ecologically and morphologically distinct genera: the widespread, species-rich and above-ground dwelling Ptychadena, the less widespread and diverse, burrowing Hildebrandtia, and the little-known, burrowing, monotypic Lanzarana, endemic to Somalia. Previous morphological studies placed Lanzarana in a sister position to Hildebrandtia and these two genera as sister to Ptychadena. However, our analyses of mitochondrial and multilocus nuclear DNA data revealed Lanzarana as a sister lineage to Ptychadena (divergence ∼28 Mya), and Hildebrandtia sister to them (∼42 Mya). This suggests that the common ancestor of ptychadenids may have exhibited a burrowing lifestyle similar to Hildebrandtia and Lanzarana, rather than the more active, above-ground lifestyle of Ptychadena. In addition, based upon analysis of available mitochondrial DNA data, we have identified major clades within the genus Ptychadena and propose them as four species groups, with the P. mascareniensis group being the first diverging lineage (∼20 Mya). We also report four new localities of Lanzarana largeni from central Somaliland, south-western Puntland, southern Somalia and south-eastern Ethiopia, extending the presently known range of the species westward. This represents the first official record of L. largeni from Ethiopia. An ecological niche model of L. largeni for present climatic conditions identifies extensive climatically highly suitable areas in central Somalia and south-eastern Ethiopia. A model for future climatic conditions estimates a substantial extension of climatically suitable areas to northern Somalia and north-eastern Kenya, likely due to predicted more humid conditions accompanying the increase of temperatures in the western Indian Ocean. [ABSTRACT FROM AUTHOR]

Societal Impact Statement Unraveling the genetic intricacies and evolutionary history of Asian Hickories through advanced genome sequencing gives valuable insights into their ecological adaptations. Understanding the impact of historical dynamics, climate fluctuations, and geographical barriers on Asian hickories not only contributes to scientific knowledge but also empowers policymakers with evidence‐based decisions and guides conservationists in their efforts to protect vulnerable species. The identification of potential habitats, especially for the endangered Carya kweichowensis, offers a promising avenue for targeted conservation efforts, aligning with global initiatives to preserve Earth's precious biodiversity, but also ensures the conservation of a vital genetic reservoir for nut‐bearing economic tree species. Summary Biogeographic characteristics of disjunct distribution play a vital role in plant geography and the endangered mechanism. The whole genome resequencing provides an opportunity to study the genetic relationship, population diffusion, and floristic evolution of disjunctive‐distribution flora. Based on the SNPs (single nucleotide polymorphisms) data generated by the whole genome deep resequencing of five EA (Eastern Asian) Carya species, we constructed the phylogenetic tree, genetic structure, and species distribution modeling to clarify the phylogenetic relationships and to predict the potential distribution area of EA Carya. Phylogenetic analysis of Carya revealed two distinct clades, separating EA Carya from NA (North America) Carya. C. kweichowensis, an endangered species, showed the lowest nucleotide diversity and the earliest divergence among studied EA Carya species. Species distribution modeling predicted suitable habitats for five EA Carya species, revealing the potential distribution of endangered C. kweichowensis. Importantly, minimal spatial overlap was observed among distribution regions of EA Carya species during different time periods. The uneven regional distribution of EA Carya is believed to be a consequence of Quaternary climate fluctuations, mountain barriers hindering species dispersal, and the limited cold tolerance of these trees. EA Carya highlights the significant role of climate and geological changes in their regional distribution and migration routes in Asia. Furthermore, the discovery of potential habitats offers a promising avenue for the conservation of C. kweichowensis.

Background: Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs of homozygosity (ROHs). Yakutian cattle are adapted to Siberia's harsh sub-arctic conditions, enduring temperatures below −70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in these cattle. Results: We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057, as compared to other breeds. Also, the different diversity indicators, namely, principal component analysis, heterozygosity, and effective population size analysis, revealed the prevalence of genetic diversity within the breed. Conclusion: Our findings on ROH are the first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity. [ABSTRACT FROM AUTHOR]

Background and Aims Amphistomy is a potential method for increasing photosynthetic rate; however, the latitudinal gradients of stomatal density across amphistomatous species and their drivers remain unknown. Methods Here, the adaxial stomatal density (SDad) and abaxial stomatal density (SDab) of 486 amphistomatous species–site combinations, belonging to 32 plant families, were collected from China, and their total stomatal density (SDtotal) and stomatal ratio (SR) were calculated. Key Results Overall, these four stomatal traits did not show significant phylogenetic signals. There were no significant differences in SDab and SDtotal between woody and herbaceous species, but SDad and SR were higher in woody species than in herbaceous species. Besides, a significantly positive relationship between SDab and SDad was observed. We also found that stomatal density (including SDab, SDad and SDtotal) decreased with latitude, whereas SR increased with latitude, and temperature seasonality was the most important environmental factor driving it. Besides, evolutionary history (represented by both phylogeny and species) explained ~10- to 22-fold more of the variation in stomatal traits than the present-day environment (65.2–71.1 vs. 2.9–6.8 %). Conclusions Our study extended our knowledge of trait–environment relationships and highlighted the importance of evolutionary history in driving stomatal trait variability. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Unraveling the genetic intricacies and evolutionary history of Asian Hickories through advanced genome sequencing gives valuable insights into their ecological adaptations. Understanding the impact of historical dynamics, climate fluctuations, and geographical barriers on Asian hickories not only contributes to scientific knowledge but also empowers policymakers with evidence‐based decisions and guides conservationists in their efforts to protect vulnerable species. The identification of potential habitats, especially for the endangered Carya kweichowensis, offers a promising avenue for targeted conservation efforts, aligning with global initiatives to preserve Earth's precious biodiversity, but also ensures the conservation of a vital genetic reservoir for nut‐bearing economic tree species. Summary: Biogeographic characteristics of disjunct distribution play a vital role in plant geography and the endangered mechanism. The whole genome resequencing provides an opportunity to study the genetic relationship, population diffusion, and floristic evolution of disjunctive‐distribution flora. Based on the SNPs (single nucleotide polymorphisms) data generated by the whole genome deep resequencing of five EA (Eastern Asian) Carya species, we constructed the phylogenetic tree, genetic structure, and species distribution modeling to clarify the phylogenetic relationships and to predict the potential distribution area of EA Carya. Phylogenetic analysis of Carya revealed two distinct clades, separating EA Carya from NA (North America) Carya. C. kweichowensis, an endangered species, showed the lowest nucleotide diversity and the earliest divergence among studied EA Carya species. Species distribution modeling predicted suitable habitats for five EA Carya species, revealing the potential distribution of endangered C. kweichowensis. Importantly, minimal spatial overlap was observed among distribution regions of EA Carya species during different time periods. The uneven regional distribution of EA Carya is believed to be a consequence of Quaternary climate fluctuations, mountain barriers hindering species dispersal, and the limited cold tolerance of these trees. EA Carya highlights the significant role of climate and geological changes in their regional distribution and migration routes in Asia. Furthermore, the discovery of potential habitats offers a promising avenue for the conservation of C. kweichowensis. [ABSTRACT FROM AUTHOR]

Psocodea is an insect order including barklice, booklice and parasitic lice. The oldest evidence of diversification in the crown group dates back to the Cretaceous, represented by a high diversity and abundance in several amber deposits. However, the Cenozoic record of psocodeans is less known. Here, we present a review of the Psocodea from the lower Eocene amber of Oise in France, including a study of 83 new specimens. The record of psocids in Oise amber is currently represented by 144 specimens corresponding to 14 species in 14 genera in 10 families of the three suborders: Trogiomorpha, Troctomorpha and Psocomorpha. The only known 'archaeatropid' Empheriidae from the Eocene, Danyazarius magnificus gen. et sp. nov., is described. In addition, the genera Annulipsyllipsocus and Sinopsyllipsocus are formally synonymized under Psyllipsocus. Wing venations of all psocid species from Oise amber are illustrated, enabling easier comparison with other taxa. A key for determination of all known psocodean species from Oise amber is given. We notice a rarity of nymphs in relation to the total number of specimens, and provide an account of known sexes, the female being more numerous than the male. We also compare the diversity with that of Baltic amber. Interestingly, Psocomorpha is the least diverse suborder in Oise amber, as in Cretaceous amber, although this suborder is the most numerous, as in current ecosystems. This study opens a window onto the evolutionary history of Psocodea during the Cenozoic and the transition to the modern‐day barklice communities. [ABSTRACT FROM AUTHOR]

Theropithecus gelada, the last surviving species of this genus, occupy a unique and highly specialised ecological niche in the Ethiopian highlands. A subdivision into three geographically defined populations (Northern, Central and Southern) has been tentatively proposed for this species on the basis of genetic analyses, but genomic data have been investigated only for two of these groups (Northern and Central). Here we combined newly generated whole genome sequences of individuals sampled from the population living south of the East Africa Great Rift Valley with available data from the other two gelada populations to reconstruct the evolutionary history of the species. Integrating genomic and paleoclimatic data we found that gene‐flow across populations and with Papio species tracked past climate changes. The isolation and climatic conditions experienced by Southern geladas during the Holocene shaped local diversity and generated diet‐related genomic signatures. [ABSTRACT FROM AUTHOR]

Freshwater ecosystems are among the most important in the world and provide essential functions and services to humans. In this study, we examine the roles of environmental and historical factors in explaining contemporary patterns of species richness. We investigated spatial patterns of species richness of freshwater crabs by compiling geographic distribution maps for 1271 species. We employed six environmental variables slightly correlated and non-collinear to test environmental hypotheses. At a global scale, we identified three regions characterized by particularly high species richness: in northern South America (Neotropical biogeographic realm), in the Western Ghats and Sri Lanka (Oriental), and southwestern China (Oriental). The best-fitting model that explained global richness variation included environmental hypotheses: Temperature-Speciation, ResourceAvailability, HabitatHeterogeneity and AnthropicImpact. We also observed a historical influence on the pattern of richness, with distinct sets of environmental predictors of richness across taxa and biogeographic realms. Our models suggest that freshwater crab richness is associated with by varying processes occurring within specific environmental and historical scenarios. In general, we documented a concentration of freshwater crab richness in areas heavily impacted by human activities. These findings hold implications for the conservation of this taxonomic group. [ABSTRACT FROM AUTHOR]

The genus Notiosorex is the only group of shrews in North America with adaptations to arid or semiarid zones. The genus was described with a single variable species, Notiosorex crawfordi , from which 5 new species have since been distinguished. To date, the phylogenetic relationships of Notiosorex species have only been partially analyzed and it is possible that there are still distinct species included within the catch-all of N. crawfordi. Here, we use geometric morphometrics on cranial and mandibular characters of the described extant species, 3 fossil species, and a distinctive population of N. crawfordi as a proxy for an integrated assessment of phylogenetic relationships of all Notiosorex species. Our results indicate that the population from the Altiplano Mexicano is more similar to, yet distinct from, N. villai than it is to N. crawfordi —we describe it as a new species. We also used the resulting tree to reconstruct phylogeographic history within the genus, which suggests that Notiosorex sp. nov. N. villai , N. evotis , and N. tataticuli all diverged allopatrically as populations from the ancestral area that is currently occupied by N. crawfordi (and in the deeper past by the fossil species N. harrisi), and pushed south into the Gulf Coast, the Altiplano, and Baja California within the last 5 million years following the end of the Miocene. [ABSTRACT FROM AUTHOR]

Leaf area varies within and between species, and previous work has linked this variation to environment and evolutionary history. However, many previous studies fail to examine both these factors and often are data‐limited.To address this, our study developed a new workflow using machine learning to automate the extraction of leaf area from herbarium collections of Australian eucalypts (Eucalyptus, Angophora and Corymbia). This dataset included 136,599 measurements, expanding existing data on this taxon's leaf area by roughly 50‐fold. Our methods were validated using field standard metrics of accuracy, and comparisons to manual measurements both from the present study and existing datasets.With this dataset for the eucalypt clade, we observed positive relationships between leaf area and mean annual temperature and precipitation similar to those reported for the global flora. However, these relationships were not consistently observed within species, potentially due to gene flow suppressing local adaptation. When we examined these relationships at different phylogenetic levels, the slope of trait–climate associations within lineages converged towards the overall eucalypt slope at shallow phylogenetic scales (5–12 MY), suggesting that effects of gene flow relax just above the species level.The strengthening of trait–climate correlations at evolutionary scales just beyond the intraspecific level may represent a widespread phenomenon across various traits and taxa. Future studies can unveil these relationships with the larger sample sizes of new trait datasets generated through machine learning.Synthesis. Using machine learning, researchers are able to confirm current positive global relationships between leaf area and mean annual temperature and precipitation. Additionally, they were able to take this a step further and examine how it changes across time. Here they saw that at roughly 5–12 million years ago in the phylogenetic tree, the trait–climate slope begins to show significantly less variation. Overall, the study shows the potential of machine learning in ecology, with exciting new potential findings with its use. [ABSTRACT FROM AUTHOR]

Aim: Species age, the elapsed time since origination, can give insight into how species longevity might influence eco‐evolutionary dynamics, which has been hypothesized to influence extinction risk. Traditionally, species' ages have been estimated from fossil records. However, numerous studies have recently used the branch lengths of time‐calibrated phylogenies as estimates of the ages of extant species. This approach poses problems because phylogenetic trees only contain direct information about species identity at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco‐evolutionary patterns derived from comparing phylogenetic age and other traits, such as extinction risk. Innovation: For bifurcating speciation, the default assumption in most analyses of species age, we propose a probabilistic approach based on the properties of a birth–death process to improve the estimation of species ages. Our approach can reduce the error by one order of magnitude under cases of high extinction and a high percentage of unsampled extant species. Main conclusion: Our results call for caution in interpreting the relationship between phylogenetic ages and eco‐evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcating speciation, we can obtain unbiased approximations of species age by combining information from branch lengths with the expectations of a birth–death process. [ABSTRACT FROM AUTHOR]

Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high‐quality single‐nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan‐Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine‐rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone‐lysine‐N‐methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest. [ABSTRACT FROM AUTHOR]

Freshwater bivalves (Bivalvia, Unionida) are one of the most threatened groups of animals in the world. Defining species boundaries and understanding the phylogeny and genetic diversity of these species is key to guiding their conservation and management. However, the presence of significant phenotypic plasticity and convergence within this group complicates species delimitation. This includes the freshwater mussel genus Nodularia, endemic to East Asia, for which a comprehensive understanding of species diversity and phylogenetic relationships remains elusive due to inadequate sampling in previous studies, particularly in China, a widely recognized biodiversity hotspot for freshwater mussels. Here, we conduct comprehensive taxonomic and phylogenetic analyses of Nodularia species based on extensive sampling across 23 provinces in China and multiple data sources, including shell morphology, soft body anatomy, six‐gene (COI + ND1 + 16S + 18S + 28S + histone H3) and mitogenome datasets. The integrative systematics approach used here reveals 10 distinct species in this genus, four of which are new to science, i.e. Nodularia hanensis sp. nov., Nodularia huana sp. nov., Nodularia fusiformans sp. nov., Nodularia dualobtusus sp. nov. and two of which are new records for China, i.e. Nodularia dorri (Wattebled [Journal de Conchyliologie, 34, 1886, 54]) and Nodularia micheloti (Morlet [Journal de Conchyliologie, 34, 1886, 75]). We also propose that the nominal species Nodularia jourdyi (Morlet [Journal de Conchyliologie, 34, 1886, 75]) syn. nov. is a new synonym for Nodularia douglasiae (Griffith & Pidgeon, 1833) based on molecular data. BI, ML, and BEAST analyses based on the six‐gene dataset and mitochondrial phylogenomics consistently support the following phylogenetic relationships: (N. dorri + (N. hanensis sp. nov. + N. micheloti)) + (N. breviconcha + (N. huana sp. nov. + (N. fusiformans sp. nov. + ((N. nuxpersicae + N. nipponensis) + (N. dualobtusus sp. nov. + N. douglasiae))))). The molecular clock with fossil calibration indicates that Nodularia originated in the Late Cretaceous period (ca. 73.78 Mya). It then diverged into two independent clades during the Middle Paleogene (ca. 45.01 Mya), followed by a rapid burst of extant speciation during the Neogene (mean age 28.28 to 4.79 Mya). Nodularia breviconcha is the earliest differentiated taxon among the 10 Nodularia taxa, appearing during the Paleogene‐Neogene transition (28.28 Mya; 95% HPD = 14.35–48.44 Mya). Taken together, we provide a robust systematic framework for Nodularia species, addressing phylogenetic relationships, taxonomy, and evolutionary history of this group. [ABSTRACT FROM AUTHOR]

Premise: Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence. Methods: We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species. Results: Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species. Conclusions: Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida. [ABSTRACT FROM AUTHOR]

The Atlantic blue crab, Callinectes sapidus, is acknowledged as one of the worst invasive alien species in the Mediterranean, impacting biodiversity and human activities. Native to the western Atlantic, it has expanded to European coastal waters since the early 1900s. Despite its ecological and commercial importance, genetic research on this species is limited. Here we show a comprehensive investigation of the genetic variation and evolutionary history in Callinectes sapidus using 667 mitochondrial COI gene sequences. Our dataset encompasses 36 newly generated sequences from previously understudied Mediterranean sites and 631 from worldwide locations obtained from the GenBank public database. Our findings reveal two distinct, but closely related, genetic groups within the species' distribution range, suggesting the occurrence of a potential species complex. Furthermore, in the Mediterranean, low levels of genetic variability were observed except for substantial haplotypic differentiation in Turkish samples. This study depicts the global genetic diversity and evolutionary patterns of Callinectes sapidus, offering new insights into the taxonomic status of the species. [ABSTRACT FROM AUTHOR]

Northwestern Argentina (NWA), together with the Pampean region (PR), has produced one of the most complete late Neogene continental sequences in Argentina. A diversity of palaeofauna has been recognized from NWA, among which glyptodonts stand out due to the high abundance of their remains. Recent evidences suggests that the Late Miocene was a period of extra-Patagonian diversification in southern South America for glyptodonts, perhaps stimulated by the expansion of C4 grasses and open environments; this has been called the as “Edad de las Planicies Australes”. Here, we focus on one of NWA's most poorly known clades of glyptodonts, the Plohophorini, from the Villavil-Quillay Basin (Catamarca Province). Our results show that, like other clades (e.g., Doedicurini), a single species can be recognized, Stromaphorus ameghini (Ameghino, 1889; ex Moreno, 1882), whose stratigraphic record spans the latest Miocene to the Pliocene (ca. 7.14–3.3 Ma; Messinian-Zanclean). Cladistic analysis confirms the status of the tribe Plohophorini as a natural group within Hoplophorinae (“austral clade”), in which S. ameghini appears as the sister species of the Pampean species S. trouessarti (Moreno, 1888) comb. nov. The oldest precise records of S. ameghini (ca. 7.14 Ma) provide a minimum age for the Plohophorini lineage. The evidence suggests that the diversity of glyptodonts from the late Neogene of NWA is composed of endemic species that are different from those of the PR; however, both areas share the same genera, as observed in other mammalian clades such as Hegetotheriidae (Notoungulata) and Dasypodidae. The cladistic analysis reveals, in a broader context, that the spine-like structure observed in the caudal tube of some genera (i.e., Nopachtus, Propanochthus, and Panochthus) is a homologous structure rather than a convergence as usually interpreted. By contrast, the similar ornamentation pattern represented by the multiplication of peripheral figures in the carapaces of the genera Stromaphorus and Nopachtus is, in fact, a convergence. [ABSTRACT FROM AUTHOR]

Urbanization is one of the leading causes of habitat loss, which has increased significantly in tropical regions in recent years, leading to the loss of species, their ecological functions, and evolutionary history. To determine the effect of urbanization on the diversity of bat communities in urban and suburban environments, we analyzed the α and β taxonomic, functional, and phylogenetic diversities at four sites along urbanization gradients surrounding a rapidly expanding city (Oaxaca City) in southern Mexico. We recorded bats using conventional techniques such as mist nets and acoustic monitoring. We calculated the diversity of bats in four sites with different urbanization conditions: urban (1), suburban (1), and rural (2). To assess the degree of total differentiation and components of bat turnover and nestedness between sites, we calculated the β taxonomic, functional, and phylogenetic diversities. A total of 33 bat species were recorded. The highest taxonomic and functional diversity was observed in the Center of Oaxaca (the site with the highest level of urbanization). In contrast, the highest phylogenetic diversity was found in the West (the site with the lowest level of urbanization). The total β taxonomic diversity was higher than the functional and phylogenetic diversity. Regarding the contributions of turnover and nestedness, turnover made a more significant contribution than nestedness to the taxonomic and phylogenetic β diversity. In contrast, functional nestedness contributed more to the functional β diversity than turnover. Tadarida brasiliensis, Desmodus rotundus, Sturnira hondurensis, and S. parvidens were recorded in all three urbanization conditions. In the most urbanized site, four Myotis species were recorded: M. fortidens, M. keaysi, M. thysanodes, and M. velifer. We suggest that the analysis of different dimensions of diversity is essential and should be considered to strengthen conservation strategies; moreover, we suggest the preservation of native vegetation mosaics and water bodies within the city to maintain bat diversity. [ABSTRACT FROM AUTHOR]

Gymnophthalmids are a diverse lineage of Neotropical lizards that present challenges in the understanding of their phylogenetic relationships and biogeographic history. Using a densely sampled phylogeny and distribution data, we investigated their biogeography at the family level. Dividing South and Central America into 12 regions, we tested six biogeographic models considering dispersal-extinction, vicariance, and founder events. Our analysis revealed high taxonomic and phylogenetic endemism in the Andes, Amazon, and Guiana Shield. The best-fit model identified the Guiana Shield as the likely ancestral area of the family, with dispersal events dominating over vicariance. Key areas for species interchange were the Amazon, Northern Andes, and Guiana Shield. The core regions of diversification included the Andes, Amazon, and Guiana Shield, with elevated species richness and biotic interchange events during the Eocene and Oligocene. The Guiana Shield stood out as a stronghold of gymnophthalmid diversity, driven by dispersal rates and ancient lineages. Our findings challenge previous hypotheses about the diversification of these lizards, suggesting a colonization pattern from lowlands to high elevations rather than the South-to-North Speciation Hypothesis for Andean lineages. [ABSTRACT FROM AUTHOR]

Background Understanding the processes that influence distribution of organisms is a major goal in evolutionary biology. Speciation in freshwater fishes is mainly associated with the “island-like” model of evolution, in which the formation of land barriers between different hydrographic basins interrupts gene flow and promotes isolation. Freshwater fish therefore provide an excellent model system for macro- and micro-evolutionary studies. The Mesa Silverside, Chirostoma jordani, is one of the most widespread freshwater fish species in the Mexican Plateau, a geologically complex physiographic region with a long history of genesis, destruction and compartmentalization of hydrographic basins that has promoted the dispersal and isolation of freshwater fishes. Methods We used mitochondrial (Cytb and D-loop) and nuclear (first intron of the ribosomal protein S7) data and used phylogeographic and coalescent based methods to elucidate the evolutionary history of C. jordani throughout its distributional range on the Mexican Plateau. Results The results obtained in the present study revealed that C. jordani consists of two main genetic groups with geographical correspondence. Clade I occur exclusively in north-western basin and shows population structure. Clade II is widely distributed across the west, central and eastern basins without population structure. The split between these two main clades was estimated at 1.4 Mya. This cladogenetic event may be associated with the allopatric process promoted by the fragmentation and compartmentalization of hydrographic basins induced by the geological and climatic history of the Mexican Plateau.

Abstract Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method that uses a novel folding force field model by exploring the intrinsic relationship between protein evolution and folding from the known protein universe. Further, the folding force field is used to guide Monte Carlo conformational sampling, driving the protein chain fold into its native state by exploring potential intermediates. On 30 example targets, FoldPAthreader successfully predicts 70% of the proteins whose folding pathway is consistent with biological experimental data.

Species are often expected to shift their distributions either poleward or upslope to evade warming climates and colonise new suitable climatic niches. However, from 18‐years of fixed transect monitoring data on 88 species of butterfly in the midwestern United States, we show that butterflies are shifting their centroids in all directions, except towards regions that are warming the fastest (southeast).Butterflies shifted their centroids at a mean rate of 4.87 km year−1. The rate of centroid shift was significantly associated with local climate change velocity (temperature by precipitation interaction), but not with mean climate change velocity throughout the species' ranges.Species tended to shift their centroids at a faster rate towards regions that are warming at slower velocities but increasing in precipitation velocity.Surprisingly, species' thermal niche breadth (range of climates butterflies experience throughout their distribution) and wingspan (often used as metric for dispersal capability) were not correlated with the rate at which species shifted their ranges.We observed high phylogenetic signal in the direction species shifted their centroids. However, we found no phylogenetic signal in the rate species shifted their centroids, suggesting less conserved processes determine the rate of range shift than the direction species shift their ranges.This research shows important signatures of multidirectional range shifts (latitudinal and longitudinal) and uniquely shows that local climate change velocities are more important in driving range shifts than the mean climate change velocity throughout a species' entire range. [ABSTRACT FROM AUTHOR]

Gymnurid rays are found in tropical, subtropical, and temperate regions around the world, where they are associated with sandy or muddy bottoms in coastal areas, being easily distinguished from other rays by the width of the disc. In recent years, the systematics of this family have been revised extensively. However, there has been no comprehensive molecular review of the family based on an adequate sample of species and localities, which may have obscured the presence of distinct evolutionary lineages. The present study was based on samples of 12 of the 13 valid species of the genus Gymnura, which were used for a multilocus reconstruction of the evolutionary history of the family Gymnuridae. Our results indicate the existence of several cryptic gymnurid lineages, within the species Gymnura micrura, Gymnura lessae, Gymnura altavela, and Gymnura poecilura. Also, we indicate that only half of the species that compose the genus are known, as well their conservation status. The analyses also indicate that the gymnurids originated during the Paleocene, with events of dispersal and vicariance occurring through the formation of oceanographic barriers, and species diversification peaking during the Oligocene and Miocene. The results of the present study reinforce the need for a comprehensive revision of the systematics of the family, in particular, the widely distributed species that are considered valid taxa, but may, in fact, represent different cryptic species. The inadequate classification of this cryptic diversity may have negative implications for the development of effective conservation measures. [ABSTRACT FROM AUTHOR]

The ability of cold-adapted bacteria to survive in extreme cold and diverse temperatures is due to their unique attributes like cell membrane stability, up-regulation of peptidoglycan biosynthesis, increased production of extracellular polymeric substances, and expansion of membrane pigment. Various cold-adapted proteins, including ice-nucleating proteins (INPs), antifreeze proteins (AFPs), cold shock proteins (Csps), and cold-acclimated proteins (CAPs), help the bacteria to survive in these environments. To sustain cells from extreme cold conditions and maintain stability in temperature fluctuations, survival strategies at the molecular level and their mechanism play significant roles in adaptations in cryospheric conditions. Furthermore, cold shock domains present in the multifunctional cold shock proteins play crucial roles in their adaptation strategies. The considerable contribution of lipopeptides, osmolytes, and membrane pigments plays an integral part in their survival in extreme environments. This review summarizes the evolutionary history of cold-adapted bacteria and their molecular and cellular adaptation strategies to thrive in harsh cold environments. It also discusses the importance of carotenoids produced, lipid composition, cryoprotectants, proteins, and chaperones related to this adaptation. Furthermore, the functions and mechanisms of adaptations within the cell are discussed briefly. One can utilize and explore their potential in various biotechnology applications and their evolutionary journey by knowing the inherent mechanism of their molecular and cellular adaptation to cold climatic conditions. This review will help all branches of the life science community understand the basic microbiology of psychrophiles and their hidden prospect in life science research. [ABSTRACT FROM AUTHOR]

Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations. [ABSTRACT FROM AUTHOR]

The genus Macaca is widely distributed, occupies a variety of habitats, shows diverse phenotypic characteristics, and is one of the best-studied genera of nonhuman primates. Here, we reported five re-sequencing Macaca genomes, including one M. cyclopis, one M. fuscata, one M. thibetana, one M. silenus, and one M. sylvanus. Together with published genomes of other macaque species, we combined 20 genome sequences of 10 macaque species to investigate the gene introgression and genetic differences among the species. The network analysis of the SNV-fragment trees indicates a reticular phylogeny of macaque species. Combining the results from various analytical methods, we identified extensive ancient introgression events among macaque species. The multiple introgression signals between different species groups were also observed, such as between fascicularis group species and silenus group species. However, gene flow signals between fascicularis and sinica group were not as strong as those between fascicularis group and silenus group. On the other hand, the unidirect gene flow in M. arctoides probably occurred between the progenitor of M. arctoides and the common ancestor of fascicularis group. Our study also shows that the genetic backgrounds and genetic diversity of different macaques vary dramatically among species, even among populations of the same species. In conclusion, using whole genome sequences and multiple methods, we have studied the evolutionary history of the genus Macaca and provided evidence for extensive introgression among the species. [ABSTRACT FROM AUTHOR]

Background: Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods: A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results: The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense. [ABSTRACT FROM AUTHOR]

Abstract Domesticated safflower (Carthamus tinctorius L.) is a widely cultivated edible oil crop. However, despite its economic importance, the genetic basis underlying key traits such as oil content, resistance to biotic and abiotic stresses, and flowering time remains poorly understood. Here, we present the genome assembly for C. tinctorius variety Jihong01, which was obtained by integrating Oxford Nanopore Technologies (ONT) and BGI-SEQ500 sequencing results. The assembled genome was 1,061.1 Mb, and consisted of 32,379 protein-coding genes, 97.71% of which were functionally annotated. Safflower had a recent whole genome duplication (WGD) event in evolution history and diverged from sunflower approximately 37.3 million years ago. Through comparative genomic analysis at five seed development stages, we unveiled the pivotal roles of fatty acid desaturase 2 (FAD2) and fatty acid desaturase 6 (FAD6) in linoleic acid (LA) biosynthesis. Similarly, the differential gene expression analysis further reinforced the significance of these genes in regulating LA accumulation. Moreover, our investigation of seed fatty acid composition at different seed developmental stages unveiled the crucial roles of FAD2 and FAD6 in LA biosynthesis. These findings offer important insights into enhancing breeding programs for the improvement of quality traits and provide reference resource for further research on the natural properties of safflower.

Abstract Background In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically. Results A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory. Conclusion Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins.

The continuous downward movement exhibited by the Lashagou landslide group in recent years poses a significant threat to the safety of both vehicles and pedestrians traversing the highway G310. By integrating geomorphological interpretation using multi-temporal optical images, interferometric synthetic aperture radar (InSAR) measurements, and continuous global navigation satellite system (GNSS) observations, this paper traced the formation period of the Lashagou landslide group, and explored its kinematic behavior under external drivers such as rainfall and snowmelt. The results indicate that the formation period can be specifically categorized into three periods: before, during, and after the construction of highway G310. The construction of highway G310 is the direct cause and prerequisite for the formation of the Lashagou landslide group, whereas summer precipitation and spring snowmelt are the external driving factors contributing to its continuous downward movement. Additionally, both the long-term seasonal downslope movement and transient acceleration events are strongly controlled by rainfall, and there is a time lag of approximately 1–2 days between the transient acceleration and heavy rainfall events. This study highlights the benefits of leveraging multi-source remote sensing data to investigate slow-moving landslides, which is advantageous for the implementation of effective control and engineering intervention to mitigate potential landslide disasters. [ABSTRACT FROM AUTHOR]

The rate and trajectory of evolution in an obligate parasite is critically dependent on those of its host(s). Adaptation to a genetically homogeneous host population should theoretically result in specialization, while adaptation to an evolving host population (i.e., coevolution) can result in various outcomes including diversification, range expansion, and/or local adaptation. For viruses of bacteria (bacteriophages, or phages), our understanding of how evolutionary history of the bacterial host(s) impacts viral genotypic and phenotypic evolution is currently limited. In this study, we used whole genome sequencing and two different metrics of phage impacts to compare the genotypes and phenotypes of lytic phages that had either coevolved with or were repeatedly passaged on an unchanging (ancestral) strain of the phytopathogen Pseudomonas syringae. Genomes of coevolved phages had more mutations than those of phages passaged on a constant host, and most mutations were in genes encoding phage tail‐associated proteins. Phages from both passaging treatments shared some phenotypic outcomes, including range expansion and divergence across replicate populations, but coevolved phages were more efficient at reducing population growth (particularly of sympatric coevolved hosts). Genotypic similarity correlated with infectivity profile similarity in coevolved phages, but not in phages passaged on the ancestral host. Overall, while adaptation to either host type (coevolving or ancestral) led to divergence in phage tail proteins and infectivity patterns, coevolution led to more rapid molecular changes that increased bacterial killing efficiency and had more predictable effects on infectivity range. Together, these results underscore the important role of hosts in driving viral evolution and in shaping the genotype–phenotype relationship. [ABSTRACT FROM AUTHOR]

An analysis of the genetic diversity of the field vole was carried out with the inclusion of new data on the complete sequences of the cytochrome b gene from the least studied area of the range of the species—the central part of Northern Eurasia (20 localities of the East European Plain, the Urals, Western and Eastern Siberia). The obtained results are generally consistent with modern view on the phylogeography of the species, but indicate the previously not investigated genetic heterogeneity of the Eastern clade, which occupies the entire Asian part of the range of the species and its European part to Northern and Eastern Europe. A comparison of the results of analysis of genetic diversity with the age of paleontological findings carried out using the Urals as an example allows one to assume that climatic changes in the Late Pleistocene and Holocene could not have led to the complete extinction of the species in the region, but to the spatial redistribution of its populations and to the complete or partial replacement of some genetic groups by others. [ABSTRACT FROM AUTHOR]

Sinojackia Hu. comprises five to eight Chinese endemic species with high ornamental and medicinal value. However, the generic limits, interspecific relationships and evolutionary history of the genus remain unresolved. In this study, we newly sequenced three plastomes of S. oblongicarpa and compared them with those of the other congeneric species to explore the taxonomic delimitation of the species and the evolutionary history of the genus. The plastome structure of Sinojackia species was extremely conserved in terms of number of genes, sequence length, and GC content. The codon usage patterns revealed that natural selection may be the main factor shaping codon usage bias. Our phylogenetic tree shows that Sinojackia is monophyletic and can be divided into two clades. Sinojackia oblongicarpa as a distinct species is supported for it is distantly related to S. sarcocarpa. The evolutionary analysis of morphological features indicates that the woody mesocarp is an ancestral feature. Sinojackia originated in central Southeast China during the early Miocene. In this period, it experienced elevated diversification and migrated from central Southeast China to the Hunan Province and the Sichuan Province with the development of the Asian monsoon and East Asian flora. Glacial–interglacial interactions with the monsoon climate may provide favorable expansion conditions for Sinojackia on a small scale. [ABSTRACT FROM AUTHOR]

Parallel evolution usually occurs among related species with similar morphological characters in adaptation to particular environments. Four wild almond species (Prunus) sharing the character of dry mesocarp splitting are distributed in China, most of which occur in arid Northwestern China. In the present study, we aimed to clarify the phylogenetic relationship, evolutionary history, and environmental adaptation of these wild almond species based on genome-wide SNP data and chloroplast genomes. Chloroplast phylogeny showed P. pedunculata and P. tenella were clustered with wild cherry species (Prunus), while P. mongolica and P. tangutica were clustered with wild peach species (Prunus). Genomic phylogeny suggested P. tenella formed an independent clade. An ABC-RF approach showed P. pedunculata was merged with P. tenella and, then, diverged from the ancestor of P. mongolica and P. tangutica. P. tenella was split from other wild almond species at ca. 7.81 to 17.77 Ma. Genetic environment association analysis showed precipitation variables contributed the most to genetic variations between P. mongolica from an arid environment and P. tangutica from a humid environment. Finally, a total of 29 adaptive loci were successfully annotated, which were related to physiological processes in response to abiotic stresses. Inconsistent genomic and chloroplast phylogenetic positions of P. tenella suggested this species could have originated from historical hybridization among different clades of Prunus. Physiological mechanisms promoted P. mongolica in adapting to the arid environment in Northwestern China. [ABSTRACT FROM AUTHOR]

Background: In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically. Results: A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory. Conclusion: Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins. [ABSTRACT FROM AUTHOR]

The Indo-Pacific eel, Anguilla marmorata Quoy & Gaimard, has the widest geographic distribution of anguillid eels. At least four populations (North Pacific, Micronesia, Indian Ocean and South Pacific) of this species were estimated to exist by previous morphological and molecular genetic studies. Recent mitochondrial control region haplotype analysis of A. marmorata eels from the eastern Caroline Islands and Guam grouped them in two separated lineages with eels from the South Pacific and western Indian Ocean. To examine the composition and possible distribution of the Micronesia population of A. marmorata that may mostly be found in the Mariana (Guam) and Caroline (Palau, Yap, Chuuk, Pohnpei, Kosrae) islands in relation to other populations in the Indo-Pacific region, we statistically compared the total number of vertebrae (TV) of specimens collected from throughout most of the range of A. marmorata including 32 specimens from Kosrae and Pohnpei islands. The TV for 1298 specimens of A. marmorata in combined data from 15 localities ranged from 100 to 110. The mean TV (107.95, 108.03) and range (105–110) of eels from the Mariana and Caroline islands were clearly higher than other localities. The post hoc multiple pairwise comparisons of the 105 pairs of single localities showed that there were 57 significant TV differences between each locality. The most significant differences were between Mariana and Caroline eels and all the other 13 localities. The statistical differences of pooled regional TV data, various genetic studies, and general geography indicate that there are likely six spawning populations of A. marmorata. This study indicates that the Caroline Islands are included in the Micronesia population, but further research is needed to understand the spawning area and life history of the Micronesia population of A. marmorata that seems to live on a relatively small number of islands in Oceania. [ABSTRACT FROM AUTHOR]

Coastal wetland ecosystems support unique biodiversity and are imminently threatened by climate change-driven sea level rise. However, the impact of climate change on their demographic and evolutionary histories is poorly understood. To improve our understanding, we examined how past climatic events have shaped the evolutionary history of the salt marsh harvest mouse (Reithrodontomys raviventris), an endangered species and a salt marsh habitat specialist, completely restricted to coastal wetlands in the San Francisco Estuary (SFE). We used whole mitochondrial genome sequences of 102 salt marsh harvest mice to characterize phylogeography and demographic history. Then, we predicted the ancient distribution of salt marsh habitat and examined correspondence between divergence, demographic history, and changes in ancient marsh habitat caused by sea level rise. A Bayesian Skyline Plot revealed demographic expansions during periods of sea level rise, particularly during the formation of the modern SFE (~ 10 kya), and rapid decline consistent with recent anthropogenic landscape change. Bayesian estimates of divergence time were consistent with subspecies divergence ~ 10 kya, and subpopulation divergence ~ 5 kya, consistent with multiple episodes of vicariance caused by Holocene sea level rise. Spatial Analysis of Molecular Variance and ΦST revealed a mismatch between the morphological and molecular subspecies assignment of two populations. Our study implicates sea level rise as a force of demographic change and evolutionary divergence in coastal marsh ecosystems. Our study also aids conservation of an endangered species by clarifying genetic subspecies boundaries and highlighting the unique nature of isolated populations that are increasingly threatened by modern sea level rise. [ABSTRACT FROM AUTHOR]