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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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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.

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]

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]

Aim Innovation Main conclusion 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.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.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]

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]

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]

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]

BACKGROUND: The harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae), native to Asia, has been introduced to other major continents where it has caused serious negative impacts on local biodiversity. Though notable advances to understand its invasion success have been made during the past decade, especially with then newer molecular tools, the conclusions reached remain to be confirmed with more advanced genomic analyses and especially using more samples from larger geographical regions across the native range. Furthermore, although H. axyridis is one of the best studied invasive insect species with respect to life history traits (often comparing invasive and native populations), the traits responsible for its colonization success in non-native areas warrant more research. RESULTS: Our analyses of genome-wide nuclear population structure indicated that an eastern Chinese population could be the source of all non-native populations and revealed several putatively adaptive candidate genomic loci involved in body color variation, visual perception, and hemolymph synthesis. Our estimates of evolutionary history indicate (1) asymmetric migration with varying population sizes across its native and non-native range, (2) a recent admixture between eastern Chinese and American populations in Europe, (3) signatures of a large progressive, historical bottleneck in the common ancestors of both populations and smaller effective sizes of the non-native population, and (4) the southwest origin and subsequent dispersal routes within its native range in China. In addition, we found that while two mitochondrial haplotypes-Hap1 and Hap2 were dominant in the native range, Hap1 was the only dominant haplotype in the non-native range. Our laboratory observations in both China and USA found statistical yet slight differences between Hap1 and Hap2 in some of life history traits. CONCLUSIONS: Our study on H. axyridis provides new insights into its invasion processes into other major continents from its native Asian range, reconstructs a geographic range evolution across its native region China, and tentatively suggests that its invasiveness may differ between mitochondrial haplotypes.

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]

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]

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]

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]

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]

The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477--0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0--0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa. [ABSTRACT FROM AUTHOR]

Simple Summary: Pampus is a genus of fish of commercial importance in Asia. This is a comprehensive study on the species delimitation and evolution history of Pampus species. This study integrated information on the skeletal structure and mitochondrial and nuclear molecular data of the genus Pampus to define their species delimitation. Based on these findings, we suggest that P. argenteus and P. echinogaster should be classified as the same species and P. liuorum is speculated to be a valid species. P. cinereus is closely related to P. minor, P. chinensis and P. punctatissimus, but these are different species. Pampus can be divided into six species: P. argenteus, P. punctatissimus, P. cinereus, P. chinensis, P. minor, and P. liuorum. The aim of this study was to resolve the controversies about the phylogeny and taxonomy of Pampus and provide a robust delimitation of Pampus for fisheries management. Pampus is a widespread species of fish in the western Pacific and Indian Oceans that has significant commercial worth. Its evolutionary history and phylogenetics are still poorly understood, and details on its intraspecific taxonomy are debatable, despite some morphological and molecular research. Here, we analyzed this species using skeletal structure data as well as nuclear (S7 gene) and mitochondrial genetic information (COI, D-loop and mitogenomes). We found that the genetic distance between P. argenteus and P. echinogaster was much smaller than that between other Pampus species, and both maximum likelihood and Bayesian phylogenetic trees yielded almost identical tree topologies. An additional and adjacent M repeat was found in the downstream region of the IQM gene cluster of P. argenteus and P. echinogaster, and the trnL2 gene of P. minor was translocated. The genus Pampus experienced early rapid radiation during the Palaeocene with major lineages diversifying within a relatively narrow timescale. Additionally, three different methods were conducted to distinguish the genus Pampus species, proving that P. argenteus and P. echinogaster are the same species, and P. liuorum is speculated to be a valid species. Overall, our study provides new insights not only into the evolutionary history of Pampus but its intraspecific taxonomy as well. [ABSTRACT FROM AUTHOR]

Artemia is a genus of halophilic zooplanktons comprising bisexual and parthenogenetic forms, which is an important model for investigating adaption to hypersaline ecosystems. The genus Artemia in China comprises four species: A. sinica, A. tibetiana, A. franciscana and A. parthenogenetica. To investigate the evolutionary relationship of bisexual and parthenogenetic Artemia in China, we analyzed the morphometrics and phylogenetics among twenty-two geographical populations in China. We found significant morphological differentiation across different species and strains of Artemia in China, which exhibited a high level of intra-population variation. We also found overlaps in morphological characteristics between populations, which may raise challenges for the classification of Artemia species using traditional morphological methods. A. franciscana, which originated from various regions in America, was generally distributed along the Chinese coastlines through multiple human introductions. Additionally, native Asian clades split into Western and Eastern Lineages during the late Miocene due to the Himalayan orogeny. Within the Western Lineage, A. tibetiana can be grouped into three taxon units: A. tibeitiana, A. sorgeloosi and A. urmiana. We also found that the distribution and genetic structure of A. sinica were influenced by climate oscillations during the Pleistocene, which might play a pivotal role in driving the formation of parthenogenetic strains in the Eastern Lineage. Overall, our study provides new insight into invertebrate evolution under geographical and climatic impacts in hypersaline environments. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) are an ancient family of signal transducers that are both abundant and consequential in metazoan endocrinology. The evolutionary history and function of the GPCRs of the decapod superfamilies of gonadotropin-releasing hormone (GnRH) are yet to be fully elucidated. As part of which, the use of traditional phylogenetics and the recycling of a diminutive set of mis-annotated databases has proven insufficient. To address this, we have collated and revised eight existing and three novel GPCR repertoires for GnRH of decapod species. We developed a novel bioinformatic workflow that included clustering analysis to capture likely GnRH receptor-like proteins, followed by phylogenetic analysis of the seven transmembrane-spanning domains. A high degree of conservation of the sequences and topology of the domains and motifs allowed the identification of species-specific variation (up to ~70%, especially in the extracellular loops) that is thought to be influential to ligand-binding and function. Given the key functional role of the DRY motif across GPCRs, the classification of receptors based on the variation of this motif can be universally applied to resolve cryptic GPCR families, as was achieved in this work. Our results contribute to the resolution of the evolutionary history of invertebrate GnRH receptors and inform the design of bioassays in their deorphanization and functional annotation. [ABSTRACT FROM AUTHOR]

Coral reefs provide a multitude of ecosystem functions owing to the high levels of biodiversity they host. Coral species, as the foundation of shallow-water reefs, differ in their contributions toward the functioning of the ecosystem due in part to the disparate phylogenetic histories of scleractinian lineages. Understanding the spatial patterns and temporal trajectories of these biodiversity facets, as well as their interrelationships, is critical for more targeted conservation strategies in the face of widespread habitat degradation and climate change. Here, we analyse long-term benthic data spanning 1986 through 2020 on coral reefs in Singapore, which have been impacted by decades of urbanisation-related and thermal stressors, to test for differences between coral biodiversity facets—specifically, taxonomic, phylogenetic (evolutionary relatedness between species), and functional (occupancy of functional trait space) richness and diversity. Analyses show that taxonomic and phylogenetic richness and diversity measures increased over the 35-year period despite declines during major bleaching events. Yet, while taxonomic and phylogenetic diversity increased, functional richness and diversity declined over the same period. Community-weighted trait measures indicate a shift towards dominance of more stress-tolerant traits such as slower growth rates, smaller corallite sizes, and massive colony forms. Together, these trends highlight the effects of chronic urban stressors alongside major bleaching events impacting reef assemblages. Critically, such assemblage shifts and functional diversity declines were masked by increasing taxonomic diversity, which is most commonly assessed, and could erode ecosystem resilience. The temporal decoupling of the biodiversity facets examined here underscore the need for more comprehensive monitoring of reefs through a combination of trait-based approaches alongside traditional field surveys at finer taxonomic resolution.

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.

Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pronounced few-tress), an online datastore and community resource for individual-level trait reporting that utilizes a semantic framework. FuTRES already stores millions of trait measurements for paleobiological, zooarchaeological, and modern specimens, with a current focus on mammals. We compare dynamically derived extant mammal species' body size measurements in FuTRES with summary values from other compilations, highlighting potential issues with simply reporting a single mean estimate. We then show that individual-level data improve estimates of body mass-including uncertainty-for zooarchaeological specimens. FuTRES facilitates trait data integration and discoverability, accelerating new research agendas, especially scaling from intra- to interspecific trait variability.

AbstractThe mitochondrial genome of Cybister brevis Aubé, 1838, is 16,198 bp long and includes 37 genes that are highly conserved in the family Dytiscidae. Phylogenetic analysis revealed that all genera in Dytiscidae, except Hydroporus and Oreodytes, are monophyletic. The Hydroporini tribe was found to be polyphyletic and closely associated with the Hygrotini, Bidessini, and Hyphydrini tribes. Dytiscinae was found to be a highly divergent polyphyletic group comprising three distinct clades. This study also revealed that C. brevis is closely related to Cybister japonicus and that the tribe Cybistrini diverged relatively early compared to other tribes in Hydroporinae. These findings are consistent with those of previous studies and provide new insights into the phylogeny of the Dytiscidae family, which has previously shown discrepancies between morphological characteristics and molecular data. The genome-level analyses conducted in this study serve as a valuable foundation for future investigations into the Dysticidae evolutionary history.

Phytoecia tigrina Mulsant (1851) is recognized as a species under strict protection EU Habitat Directive, it represents a focal point for conservation efforts across Europe. However, the dearth of comprehensive understanding regarding its biology, ecology, and geographical distribution poses formidable challenges to conservation endeavors. In the current study, we have delineated eight European and two Asian distinct metapopulations of Ph. tigrina across its geographic range, with a particular emphasis on elucidating its dispersion within the Circum-Carpathian region. This delineation serves to underscore the species' distribution, niche dimensions and limits of ecological tolerance that illuminate its adaptation capacity to diverse environmental conditions within the range. Our study has unveiled notable differentials in both morphological and ecological traits among Ph. tigrina metapopulations, notably between those located on the eastern and western flanks of the Carpathian Arc. Such differentials suggest the influence of divergent evolutionary trajectories, likely influenced by historical climatic changes during the Late Pleistocene and Holocene epochs. Significantly, specimens derived from eastern metapopulations exhibit morphological features of sufficient magnitude to warrant the proposition of a distinct subspecies, Phytoecia (Pilemia) tigrina podillica ssp. nov. This taxonomic delineation underscores the taxonomic complexity inherent within the Ph. tigrina species complex. Our investigations have further illuminated the historical dynamics of the species distribution, indicating the presence at least of two refugia during the Last Glacial Maximum (LGM). These refugial enclaves, situated in the Sea of Marmara/Eastern Aegean Sea region and the Pannonian Plain, likely played pivotal roles in shaping contemporary distributional patterns. Moreover, our ecological niche modeling endeavors have elucidated rapid expansions of suitable habitat for Ph. tigrina during post-glacial epochs, notably the Preboreal and Boreal periods. These expansions aligned with the rapid dispersion of its host plant Cynoglottis barrelieri supplying colonization of new territories in the face of the fast-changing post-glacial environment. Our study underscores the intricate interplay between evolutionary history, environmental dynamics, and imperatives for conservation Ph. tigrina. By elucidating these complexities, we endeavor to furnish a robust foundation for future conservation initiatives aimed at safeguarding this emblematic species and its associated habitats.

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.

Aim: The Neotropics constitute the most biodiverse region of the world, yet its patterns of diversification and speciation differ among Neotropical areas and are not equally well understood. Particularly, avian evolutionary processes are understudied in the open habitats of temperate South America, where the role of glacial cycles is not clear. We analysed the evolutionary history of a Neotropical widespread bird species as a case study to evaluate its continental‐scale patterns and processes of diversification, with a focus on Patagonia. Location: Open habitats of the Neotropics. Taxon: Vanellus chilensis (Aves, Charadriiformes). Methods: We obtained reduced representation genomic and mitochondrial data from the four subspecies of V. chilensis to perform a phylogenetic/phylogeographical analysis and study the evolutionary history of the species. We complemented these analyses with the study of vocalizations, a reproductive signal in birds. Results: The initial diversification event within V. chilensis, approximately 600,000 years ago, split a Patagonian lineage from one containing individuals from the rest of the Neotropics. We found considerable gene flow between these two lineages and a contact zone in northern Patagonia, and showed that genomic admixture extends to northwestern Argentina. Shallower divergence was detected between the two non‐Patagonian subspecies, which are separated by the Amazon River. Vocalizations were significantly different between the two main lineages and were intermediate in their temporal and frequency characteristics in the contact zone. Main Conclusions: Patagonian populations of V. chilensis are clearly differentiated from those of the rest of the Neotropics, possibly as a consequence of Pleistocene glaciations. A secondary contact zone in northern Patagonia with extensive gene flow among lineages appears to be the consequence of post‐glacial, northward expansion of the Patagonian populations. Future analyses focused on the dynamics of the contact zone will allow us to establish whether the species continues to diverge or is homogenizing. [ABSTRACT FROM AUTHOR]

The mitochondrial genome of Cybister brevis Aubé, 1838, is 16,198 bp long and includes 37 genes that are highly conserved in the family Dytiscidae. Phylogenetic analysis revealed that all genera in Dytiscidae, except Hydroporus and Oreodytes, are monophyletic. The Hydroporini tribe was found to be polyphyletic and closely associated with the Hygrotini, Bidessini, and Hyphydrini tribes. Dytiscinae was found to be a highly divergent polyphyletic group comprising three distinct clades. This study also revealed that C. brevis is closely related to Cybister japonicus and that the tribe Cybistrini diverged relatively early compared to other tribes in Hydroporinae. These findings are consistent with those of previous studies and provide new insights into the phylogeny of the Dytiscidae family, which has previously shown discrepancies between morphological characteristics and molecular data. The genome-level analyses conducted in this study serve as a valuable foundation for future investigations into the Dysticidae evolutionary history. [ABSTRACT FROM AUTHOR]

Sequence capture is a genomic technique that selectively enriches target sequences before high throughput next-generation sequencing, to generate specific sequences of interest. Off-target or ‘bycatch’ data are often discarded from capture experiments, but can be leveraged to address evolutionary questions under some circumstances. Here, we investigated the effects of missing data on a variety of evolutionary analyses using bycatch from an exon capture experiment on the global pest moth, Helicoverpa armigera. We added > 200 new samples from across Australia in the form of mitogenomes obtained as bycatch from targeted sequence capture, and combined these into an additional larger dataset to total > 1000 mitochondrial cytochrome c oxidase subunit I (COI) sequences across the species’ global distribution. Using discriminant analysis of principal components and Bayesian coalescent analyses, we showed that mitogenomes assembled from bycatch with up to 75% missing data were able to return evolutionary inferences consistent with higher coverage datasets and the broader literature surrounding H. armigera. For example, low-coverage sequences broadly supported the delineation of two H. armigera subspecies and also provided new insights into the potential for geographic turnover among these subspecies. However, we also identified key effects of dataset coverage and composition on our results. Thus, low-coverage bycatch data can offer valuable information for population genetic and phylodynamic analyses, but caution is required to ensure the reduced information does not introduce confounding factors, such as sampling biases, that drive inference. We encourage more researchers to consider maximizing the potential of the targeted sequence approach by examining evolutionary questions with their off-target bycatch where possible—especially in cases where no previous mitochondrial data exists—but recommend stratifying data at different genome coverage thresholds to separate sampling effects from genuine genomic signals, and to understand their implications for evolutionary research. [ABSTRACT FROM AUTHOR]

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alalā were more numerous, to samples taken between 1973 and 1998, when 'Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains. [ABSTRACT FROM AUTHOR]

Extensins (EXTs), a class of hydroxyproline-rich glycoprotein with multiple Ser-Pro3–5 motifs, are known to play roles in cell wall reinforcement and environmental responses. EXTs with repetitive Tyr-X-Tyr (YXY) motifs for crosslinking are referred as crosslinking EXTs. Our comprehensive study spanned 194 algal and plant species, categorizing EXTs into seven subfamilies: classical extensins (EXT I and II), arabinogalactan-protein extensins (AGP-EXTs), proline-rich extensin-like receptor kinases (PERKs), leucine-rich repeat extensins (LRX I and II), formin homology (FH) domain-containing extensins (FH-EXTs), proline-rich, arabinogalactan proteins, conserved cysteines (PAC) domain-containing extensins (PAC I and II), and eight-cysteine motif (8CM)-containing extensins (8CM-EXTs). In the examined dataset, EXTs were detected ubiquitously in plants but infrequently in algae, except for one Coccomyxa and four Chlamydomonadales species. No crosslinking EXTs were found in Poales or certain Zingiberales species. Notably, the previously uncharacterized EXT II, PAC II, and liverwort-specific 8CM-EXTs were found to be crosslinking EXTs. EXT II, featuring repetitive YY motifs instead of the conventional YXY motif, was exclusively identified in Solanaceae. Furthermore, tandem genes encoding distinctive 8CM-EXTs specifically expressed in the germinating spores of Marchantia polymorpha. This updated classification of EXT types allows us to propose a plausible evolutionary history of EXT genes during the course of plant evolution. [ABSTRACT FROM AUTHOR]