Search Results (388)

The systematics and phylogeny of the most speciose genus (Leopardus) of the felidae have historically been contentious and problematic. These issues have been compounded with the recent advancement of genetic techniques that make it possible to detect events such as incomplete lineage sorting (ILS), punctual historical ancestral introgression (PHAI), and repetitive introgression or recent hybridization (RI-RH). Each of these events have noteworthily affected the Leopardus genus. One Leopardus taxon (Leopardus tigrinus, herein called tigrina) has been especially complex from a phylogenetic point of view. In the last decade, one new species has been reported (L. guttulus) and two other new species likely exist within the tigrinas (L. emiliae and L. pardinoides). However, the most surprising find was the discovery of a new and not previously reported tigrina, the Nariño cat, from the southern Andean region of Colombia (2023). Later that same year, a new paper criticized the discovery. In response to that criticism, herein, we provide new molecular genetics results of the Nariño cat as well as new insights into the molecular phylogeny of the tigrinas inside the Leopardus genus: (1) In this new work, we analyzed the mtND5 gene of Nariño cat samples collected over four years (2001, 2007, 2017, 2023) as well as analyzed mitogenomes of Nariño cat samples collected in three different years (2001, 2017, 2023). The temporal Nariño cat samples (2001, 2007, 2017, 2023) refer to samples taken from a single specimen across different years. Based on these analyses, data from 2001 and 2007 represent the most reliable information. In contrast, samples from 2017 and 2023 may be contaminated with DNA from the Pampas cat and tigrina, respectively. (2) On the other hand, based on sequencing the mtND5 gene of 164 specimens of Leopardus, northern Andean and Central American tigrinas (37 specimens) are divided into at least six different groups (without counting the Nariño cat). Based on our analysis of sequenced mitogenomes of 102 specimens (including 34 northern Andean and Central American tigrinas) of the Leopardus genus, there are at least eight different groups of tigrinas (without counting the Nariño cat). Henceforth, there are strong datasets which support the existence of multiple lineages within the presumed “a priori” northern Andean tigrina and thus much of the genetic diversity of this wild cat has gone unnoticed. There are a series of potential taxa that have gone unnoticed due to a lack of sampling of this polyphyletic Andean feline. Full article

Highly pathogenic avian influenza (HPAI) H5N1 continues to pose a major threat to animal and public health. Since its emergence, clade 2.3.4.4b has become the dominant global lineage, associated with widespread outbreaks in Europe. This study aimed to characterise the H5N1 strains detected in backyard chickens in Serbia and investigate their phylogenetic and phylogeographic relationships with historical and currently circulating strains in Serbia and the broader region. Samples collected in 2024 were tested by qRT-PCR, and positive samples were propagated in MDCK cells. Whole genome sequencing of isolated virus was performed using the MinION Mk1C platform (ONT, Oxford, UK). Bayesian phylogenetic and phylogeographic analyses were conducted using BEAST X and SPREAD3 v.9.6. The results revealed three independent introductions of H5N1 into Serbia between 2020 and 2024. The spatiotemporal diffusion patterns confirmed both north–south and west–east viral spread from Northern and Central Europe into the Balkans. Additionally, Serbia was identified as a critical transit and divergence point in the regional transmission network, highlighting its role in the spread of H5N1 between Western and Eastern Europe. These findings underscore the importance of continued genomic surveillance in both domestic and wild bird populations to better understand and reduce HPAI spread. Full article

Perkinsiodendron macgregorii, an endangered Chinese endemic tree with high ornamental and ecological value, faces extinction threats due to its poor natural regeneration and habitat degradation. Despite the urgent need for its conservation, the genetic architecture and population differentiation mechanisms of this taxon remain poorly understood, hindering science-based protection strategies. We conducted comprehensive chloroplast genomic analyses of 134 individuals from 13 natural populations to inform science-based conservation. The chloroplast genome (158,538–158,641 bp) exhibited conserved quadripartite organization, with 113 functional genes and elevated GC contents in IR regions (42.99–43.02%). Population-level screening identified 741 SNPs and 678 indels, predominantly in non-coding regions (89.8%), with three distinct phylogeographic clades revealing north-to-south genetic stratification. The northern clade (Clade A) demonstrates the highest haplotype diversity and nucleotide diversity, followed by the southern clade (Clade C), while the central clade (Clade B) exhibits signals of genetic erosion (Tajima’s D > 3.43). Based on the genetic diversity distribution and phylogenetic tree of extant P. macgregorii, we inferred that the northern populations represent ancestral groups, while the Wuyi Mountains region and Nanling Mountains region served as glacial refugia. It is imperative to implement in situ conservation in these two regions. Additionally, ex situ conservation should involve collecting seed from representative populations across all three clades and establishing isolated cultivation lines for each clade. These findings establish a genomic framework for conserving endangered plants. Full article

Türkiye represents an important biogeographic region connecting Southeast Europe with Southwest Asia, where pig domestication began in the western Palearctic. We studied the phylogenetic relationships and spatial distribution of new and published mitochondrial D-loop sequences of wild boars from Türkiye, other parts of the Middle East, and from around the world to understand migration patterns within Asia Minor and other parts of the Middle East as well as across the Bosphorus/Sea of Marmara/Dardanelles, a current migration barrier to Southwest Europe. Our phylogenetic (ML, BI) and spatial (Geneland) analyses revealed haplotypes both endemic to Anatolia and with a wider distribution in the Middle East as well as European (E1) lineages. The latter suggested possible rare immigration into Anatolia at present times and prehistorical/historical anthropogenic translocations of wild boars or pigs, such as during the pre-Hellenic, Roman, and Byzantine periods or during the European crusades, and subsequent introgression into Anatolian wild boars. Import of pigs with E1 haplotypes and introgression into wild boars during the medieval Empire of Trebizond particularly by Italian merchants or settlers, is also suggested. Anatolian lineages that may have formed the basis of the archaic domestication process of pigs in the western Palearctic are discussed. Full article

The diverse topography and mild monsoon climate in East Asia are considered to be important drivers for the long-term ecological success of the Tertiary relict ‘living fossil’ plants during the glacial/interglacial cycles. Here we investigated the phylogeographic pattern and demographic history of a hamamelidaceous Tertiary relict ‘living fossil’ tree (Parrotia subaequalis) endemic to the subtropical forests of eastern China, employing molecular data and ecological niche modeling. In the long evolutionary history, P. subaequalis has accumulated a high haplotype diversity. Weak gene flow by seeds, geographical isolation, and heterogeneous habitats have led to a relatively high level of genetic differentiation in this species. The divergence time of two cpDNA lineages of P. subaequalis was dated to the late Miocene of the Tertiary period, and the diversification of haplotypes occurred in the Quaternary period. Paleo-distribution modeling suggested that P. subaequalis followed the pattern of ‘glacial expansion-interglacial compression’. The Dabie Mountain and Yellow Mountain in Anhui Province and the Tianmu Mountain and Simin Mountain in Zhejiang Province were inferred to be multiple glacial refugia of P. subaequalis in East Asia and have been proposed to be protected as ‘Management Units’. Collectively, our study offers insights into the plant evolution and adaptation of P. subaequalis and other Tertiary relict ‘living fossil’ trees endemic to East Asia refugia. Full article

The fossil and molecular evidence suggests that the area of origin of the Hairy Armadillo Chaetophractus villosus was the central Pampas region of Argentina, with a current distribution that includes Bolivia, Paraguay and Chile. We studied the evolutionary history of peripheral individuals of C. villosus using phylogeographic approaches and potential distribution models for the Holocene. We sequenced a segment of the mitochondrial DNA control region in 22 individuals with a peripheral distribution that inhabit the western limit of its current distribution in Chile, which was compared with Argentine sequences of the central distribution. The results show that the peripheral individuals studied have less genetic polymorphism than populations in the central distribution. All Chilean sequences were grouped in the haplotype C, which is dominant in Patagonian populations of Argentina. The potential distribution model predicts that during the Holocene the areas in which the peripheral populations of Chilean C. villosus are currently distributed presented medium–high habitability conditions for the species. Our results are consistent with the center–periphery model, showing a decrease in genetic diversity in peripheral areas of the distribution of C. villosus. It is probable that the low genetic diversity of the peripheral population is related to recent population establishment by dispersion from adjacent Argentine Patagonian populations. Peripheral populations such as those studied can have small population sizes; however, they can remain stable and have high survival rates during climatic oscillations, acting as important relics for the conservation and evolutionary potential of the species. Full article

Giant clams are ecologically important coral reef animals, with many species facing imminent local extinction. While many regions have undertaken recent assessments of their biodiversity assets, persistent gaps remain even in otherwise well-surveyed areas. This study sought to understand the geographic distribution of smaller-bodied and morphologically similar giant clams, specifically Tridacna maxima and T. noae, in the eastern Indian Ocean. Due to the difficulties in reliably identifying these species using morphological characters, we confirmed species identity and investigated intraspecific variation using sequence data from the mitochondrial cytochrome C oxidase subunit I gene (COI). Seventy whole animal vouchers were newly sampled from a 1500 km span of remote northwestern Australian coastline over a decade, as part of an ongoing coral reef survey expedition of the Western Australian Museum and partners. Tridacna maxima had a limited distribution and was only genotyped from offshore oceanic reefs in the Rowley Shoals and Cocos Keeling Islands. In contrast, T. noae was well established beyond Ningaloo Reef, and was abundant at inshore sites throughout the Pilbara and Kimberley, and even offshore to Ashmore Reef. Phylogeographically, T. maxima did not group with conspecifics from the Western Pacific Ocean, including the east coast of Australia, but instead clustered with individuals from Malaysia, China, Taiwan, and Indonesia; T. noae exhibited a similar pattern. The affinity of Western Australian individuals with representatives from the Indo-Malay region and not eastern Australia will be an important consideration for these commercially important species. Novel haplotypes in both tested species occur in Western Australia. Continued sampling of eastern and central Indian Ocean giant clams, especially to continue to document the range of T. noae, is encouraged to understand connectivity in this basin. Together, these findings contribute to an improved baseline for conservation initiatives of these iconic coral reef animals in Western Australia. Full article

The Japanese encephalitis virus is an arbovirus that causes severe damage to the central nervous system. At present, there are still 67,900 cases of Japanese encephalitis worldwide every year, which poses a global public health concern and causes great economic losses to animal husbandry. In this study, we analyzed the epidemiology, transmission, and evolution of JEV based on the NCBI database. E and NS1 were emphatically analyzed for amino acid variation and predicted protein structure. Gene recombination and the evolutionary rate of JEV were analyzed using RDP 4 and BEAST. The maximum clade credibility tree of E was reconstructed to estimate the time of the most recent common ancestor. Chinese genotype Ⅰ (GI) strain recombination events occurred in the C, M/PrM, E, NS2A, NS4B, and NS5 proteins, and genotype III (GIII) strains occurred in the E, NS1, NS3, NS4A, and NS5 proteins. The average evolutionary rates of JEV were comparable (3.3830 × 10⁻⁴, 2.0481 × 10⁻⁴, 3.5650 × 10⁻⁴, 2.2423 × 10⁻⁴, 3.0844 × 10⁻⁴, and 1.9757 × 10⁻⁴ substitutions/site/year for the JEV-I whole genome, JEV-III whole genome, JEV-I E gene, JEV-III E gene, JEV-I NS1 gene, and JEV-III NS1 gene, respectively). The MCC tree revealed the evolutionary order was GⅢ, GⅠ, GⅤ, GⅡ, and GⅣ. This study was expected to provide theoretical support for vaccine development and comprehensive prevention and treatment of JEV. Full article

Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus. Full article

A characteristic feature of influenza A viruses is their high capacity for reassortment, significantly increasing their genetic diversity. This can lead to the formation of influenza A virus variants with unique phenotypic characteristics, particularly those with pandemic potential. Representatives of the H4N9 subtype are low-pathogenic influenza A (LPAI) viruses. Despite their low pandemic potential, these viruses may represent an important reservoir of genes for genetic exchange with other IAVs. Here, we analyzed the reassortment events of H4N9 viruses using all publicly available sequences. Several computational approaches, including phylogenetic reconstructions and reassortment detection algorithms (PDDM and PDCP), were used to identify phylogenetic incongruences. Numerous reassortment events were detected in H4N9 viruses, especially in the NS segment. This suggests extensive genetic exchange with other avian and mammalian IAVs. In addition, a comparison of phylogenetic and geographic patterns suggests that H4N9 viruses have undergone multiple trans-regional transmissions. These results suggest that LPAI viruses make a significant contribution to the overall influenza gene pool, increasing the likelihood of the emergence of new IAV variants with unpredictable phenotypic characteristics. However, our results suggest that the current understanding of the real distribution and genetic diversity is fragmented. Therefore, better monitoring and surveillance of H4N9 viruses should improve influenza pandemic preparedness. Full article

Tomato leaf curl Palampur virus (ToLCPalV) is an economically important bipartite begomovirus in the agro-ecological regions in south and western Asia. This study was designed to investigate the sequence variation dynamics, regional delineation, genetic diversity, population structure, and cross-border dispersal patterns of ToLCPalV. The research revealed clear geographical structuring, with distinct Indo–Pak subcontinent and Middle Eastern clades, but no host-specific differentiation. Genetic diversity analysis indicated higher diversity in the Indo–Pak subcontinent, particularly in the DNA-B component, suggesting an older, more diverse population of ToLCPalV prevailing in this region. Neutrality tests and selection pressure analyses revealed predominantly purifying selection, with limited positive selection observed in BV1 of DNA-B. The primary source of dispersal of ToLCPalV progenitor was estimated in Varnasi, India in 1955, from where the virus was spread. No recombination events were detected, suggesting that mutation and selection are the primary drivers of ToLCPalV evolution. Furthermore, a detailed SDT-based nucleotide sequence comparison analysis also identified two potential strains of ToLCPalV. This study elucidates the spatiotemporal dynamics and evolutionary history of ToLCPalV, revealing its cross-border spread and adaptive evolution. These findings contribute to a more comprehensive understanding of begomovirus epidemiology and provide valuable insights into ToLCPalV’s phylogeography and evolutionary dynamics. Full article

The genealogical and geographical distribution of a species offers insights into its evolutionary narrative, encompassing its population dispersion, migration, adaptation, and speciation—key aspects for comprehending the genesis and sustenance of biodiversity. Using three mitochondrial genes on 115 samples, this study examined the phylogeographic structure, phylogenetic divergence, and environmental evolution of the viviparous multiocellated racerunner (Eremias multiocellata) in the Tarim Basin of China. Our analyses revealed a significant phylogenetic structure and suggested that the distributed populations began to diverge approximately 6.63 million years ago (Ma), influenced by the uplift of surrounding mountain ranges and glacial cycles, and further differentiated into distinct groups around 3.72 Ma–1.50 Ma, exhibiting genetic distinctions. These results supplement the foundational genetic data to the Tarim Basin and provide insights on how historical geological events affect the species distribution and genetic differentiation and species formation in this region. Full article

Moricandia moricandiodes is an endemic species found in the south and east of the Iberian Peninsula. Five subspecies have been recognized, and all exist as fragmented populations on limestones and marls with salt and gypsum intrusions under a continental Mediterranean climate, except for one of the subspecies, which inhabits semi-arid and hotter environments. In this study, we sampled populations covering the distribution area of the species and performed a population and phylogeographic study to assess the evolutionary history of populations and the taxonomic relationships of subspecies. ISSR markers, nrITS, and plastid sequences were used in the analyses. The results revealed that, in general, southern populations showed higher genetic diversity than northern populations, suggesting that the former are located in glacial refugia. Furthermore, we did not find clear differences between subspecies, except for M. moricandioides subsp. pseudofoetida, which showed exclusive haplotypes and an exclusive ribotype. Isolation and rapid divergence are discussed as the probable causes of differentiation, whereas bottlenecks and secondary contact between populations would explain the absence of differentiation among the other subspecies. Finally, we propose a few guidelines for the conservation of M. moricandioides. Full article

Sargassum hemiphyllum var. chinense is a common brown seaweed along the southeastern coast of China, playing a significant ecological role and possessing considerable resource utilization value. However, its genetic diversity and phylogeographic patterns remain poorly understood. In this study, we employed multiple molecular markers, including the nuclear ITS sequence (ribosomal internal transcribed spacer), the plastid rbcL gene (encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase), and the mitochondrial cox3 and cox1 genes (encoding cytochrome c oxidase subunits III and I, respectively), to elucidate the genetic and phylogeographic structure of S. hemiphyllum var. chinense. Our findings demonstrate that the combined use of plastid and mitochondrial gene sequences is suitable for phylogeographic studies of this species. Genetic structure difference was observed among 15 populations which localities covering most of its distribution range, likely resulting from colonization by ancestors of different origins and limited gene flow among populations. The study revealed two distinct lineages of S. hemiphyllum var. chinense, exhibiting a north–south geographical distribution with a mixed zone in the southern Fujian–eastern Guangdong coastal region. These lineages are inferred to have diverged during the Middle to Late Pleistocene due to the isolation of the East China Sea and South China Sea during glacial periods. Sub-lineage differentiation was also detected within the northern lineage. The southern lineage experienced demographic expansion following the end of the Last Glacial Maximum, while the northern lineage remained stable. The southern Fujian–eastern Guangdong region, characterized by high genetic diversity, may have served as a glacial refugium or a contact zone for the post-glacial recolonization of the two lineages. Global warming may lead to range contraction and reduced genetic diversity in this species. The high genetic diversity area should be prioritized for conservation efforts. Overall, these findings provide insights into the genetic structure status and causes of S. hemiphyllum var. chinense and offer a scientific basis for proposing reasonable measures for its resource management. Full article

This study aimed to reveal intraspecific variations in two Dryomys species distributed in Türkiye, based on mitochondrial DNA cytochrome b gene sequences, and to discuss the factors driving these variations in the context of phylogeography and genetic species concepts. As a result of Maximum Likelihood, Bayesian Inference, and Network analyses, which included haplogroups or lineages from Italy, Russia, the Caucasus, and Iran identified in previous studies, along with Turkish haplotypes, three major clades (MC1, MC2, and MC3) were identified within Dryomys nitedula. These clades began to diverge evolutionarily in the middle of the Late Miocene (8.82 million years ago) and exhibit significant genetic differences from one another. The Turkish haplotypes were divided into five distinct lineages (N1–N5), each within five subclades (SC1–SC5), which were nested within these MCs. These lineages, their geographical distributions, and the subspecies defined in previous studies that correspond to these lineages are as follows: N1 from the Thrace region (Dryomys nitedula wingei), N2 from the Black Sea region (potentially a new subspecies), N3 from western and central Anatolia (Dryomys nitedula phrygius), N4 from northeastern Anatolia (Dryomys nitedula tichomirowi), and N5 from eastern Anatolia (Dryomys nitedula pictus). The N2 lineage, distributed in areas close to the coastal side of the Eastern Black Sea region and with a range close to both N3 (D. n. phrygius) and N4 (D. n. tichomirowi), exhibited high genetic differentiation from these two lineages and was a candidate to be treated as a new subspecies of Dryomys nitedula in Türkiye. The N5 lineage, which includes haplotypes from the distribution areas of the populations initially classified as Dryomys pictus and later as Dryomys nitedula pictus in previous studies, was found to be more closely related to Dryomys nitedula kurdistanicus from the Zagros Mountains than to D. n. pictus from the central regions of Iran. Combining the results of this study with previous research, it is clear that the D. nitedula lineages in Türkiye, along with haplogroups or subspecies in neighboring regions diverged between the middle Late Miocene and Middle Pleistocene. This divergence is believed to have been driven by climatic cycles and geomorphological processes that shaped the topography of their distribution range. The high genetic diversity observed in the lineages of Anatolia suggests that the region may have served as a glacial refuge for D. nitedula. Similarly to the processes and factors shaping the evolution of D. nitedula, Dryomys laniger was found to have diverged into two lineages, western (L1) and eastern (L2 or Dryomys anatolicus), within its distribution range during the Late Pliocene (2.94 Mya). To make a more accurate taxonomic assessment of D. laniger, a larger number of samples is needed, and the distribution limits should be more clearly defined. Full article