Search Results (39)

Identifying the diversity of wildlife hosts for malaria parasites in wildlife is crucial for understanding transmission dynamics in endemic regions where humans, vectors, and wildlife heavily overlap. We examined the presence of Plasmodium parasites in free-ranging ring-tailed coatis (Nasua nasua, n = 44) and nine-banded armadillos (Dasypus novemcinctus, n = 66) from an Indigenous community in the Peruvian Amazon. Nested PCR targeting the mitochondrial cytb gene detected Plasmodium spp. DNA in two coatis (4.7%). Sequencing revealed one lineage identical to Plasmodium vivax/P. simium and another to P. malariae/P. brasilianum. A subset of samples was reanalyzed using cox3-based PCR and sequencing in an independent laboratory, confirming P. malariae/P. brasilianum in one coati. No infections were observed in armadillos. These results indicate that coatis in the wild may host diverse Plasmodiidae parasites and that coatis may even carry Plasmodium spp., likely as incidental hosts. Expanding surveillance to additional non-primate mammals will help clarify their role in sylvatic malaria ecology and evaluate potential zoonotic risks. Full article

Pink salmon, Oncorhynchus gorbuscha, introduced to the White Sea and expanded throughout the West Arctic and Northern Atlantics, represents a noteworthy example of a successful marine species introduction that has significantly impacted the local fish community. In our study, we analysed mitochondrial cytochrome b sequences from 635 individuals, representing both odd-year (n = 411) and even-year (n = 224) spawning lineages. These samples were collected from rivers in the White, Barents, Kara, and Northern seas, as well as from source populations in the Pacific. Fifteen cytb haplotypes were identified in the odd-year spawning lineage and twenty-six in the even-year lineage, with only ten haplotypes found in both lineages. The results demonstrated significant genetic differences between the native Pacific populations and the introduced Arctic populations in the odd-year lineage. In contrast, no genetic differentiation was found in the even-year lineage. This study describes the current haplotypic structure of European pink salmon in the Russian Arctic and provides insights into the genetic consequences of the species’ introductions. Full article

African ground squirrels (Xerus spp.), the inhabitants of African arid zones, face extreme heat and water scarcity driving selection for metabolic optimization. We assembled and annotated the first mitogenomes of Xerus inauris and Xerus rutilus (16,525–16,517 bp), revealing conserved vertebrate architecture with genus-specific traits. Key features include Xerus rutilus’s elongated ATP6 (680 vs. 605 bp), truncated ATP8–ATP6 spacers (4 vs. 43 bp), and tRNA-Pro control regions with 78.1–78.3% AT content. Their nucleotide composition diverged from that of related sciurids, marked by reduced T (25.78–26.9%) and extreme GC skew (−0.361 to −0.376). Codon usage showed strong Arg-CGA bias (RSCU = 3.78–3.88) and species-specific elevations in Xerus rutilus’s UGC-Cys (RSCU = 1.83 vs. 1.17). Phylogenetics positioned Xerus as sister to Ratufa bicolor (Bayesian PP = 0.928; ML = 1.0), aligning with African biogeographic isolation. Critically, we identified significant signatures of positive selection in key mitochondrial genes linked to arid adaptation. Positive selection signals in ND4 (ω = 1.8 × background), ND1, and ATP6 (p < 0.0033) correspond to enhanced proton gradient efficiency and ATP synthesis–molecular adaptations likely crucial for optimizing energy metabolism under chronic water scarcity and thermoregulatory stress in desert environments. Distinct evolutionary rates were observed across mitochondrial genes and complexes: Genes encoding Complex I subunits (ND2, ND6) and Complex III (Cytb) exhibited accelerated evolution in arid-adapted lineages, while genes encoding Complex IV subunits (COXI) and Complex V (ATP8) remained highly conserved. These findings resolve the Xerus mitogenomic diversity, demonstrating adaptive plasticity balancing arid-energy optimization and historical diversification while filling critical genomic gaps for this xeric-adapted lineage. Full article

Castor fiber birulai is a subspecies of the Eurasian beaver that has a relatively small population size compared to other Castor subspecies. There is limited genetic research on this subspecies. In this study, mitochondrial cytochrome b (Cytb) and D-loop sequences were analysed in genetic samples obtained from 19 individuals residing in the Buergen River Basin, Xinjiang, China. The Cytb region presented a single haplotype, whereas three haplotypes were identified in the D-loop region. The genetic diversity within the Chinese population was low (D-loop Hd = 0.444; Pi = 0.0043), markedly lower than that observed in other geographical populations of C. fiber. Phylogenetic reconstructions and haplotype network analyses revealed substantial genetic differentiation between C. f. birulai and other Eurasian lineages (Fst > 0.95), supporting the status of C. f. birulai as a distinct evolutionary lineage. Although the genetic distance between the Chinese and Mongolian populations was relatively small (distance = 0.00269), significant genetic differentiation was detected (Fst = 0.67055), indicating that anthropogenic disturbances—such as hydraulic infrastructure and fencing along the cross-border Bulgan River—may have impeded gene flow and dispersal. Demographic analyses provided no evidence of recent population expansion (Fu’s Fs = 0.19152), suggesting a demographically stable population. In subsequent studies, we recommend increasing nuclear gene data to verify whether the C. f. birulai population meets the criteria for Evolutionarily Significant Unit classification, and strengthening cross-border protection and cooperation between China and Mongolia. Full article

The alpine musk deer (Moschus chrysogaster) is a critically endangered species in China whose wild populations have precipitously declined due to habitat degradation and poaching. In response, China established the world’s first captive breeding facility for this species in 1990. Despite over three decades of closed breeding, the genetic consequences of long-term captivity remain unclear. Here, we present the first comprehensive assessment of mitochondrial genetic diversity in a captive population of 409 individuals, using three mitochondrial markers (D-loop, Cytb, and COI) and comparative data from wild conspecifics. Our results reveal a pronounced reduction in genetic diversity in the captive population compared to wild populations. Nucleotide diversity (π) and haplotype diversity (Hd) were consistently lower across all markers in captivity, with D-loop Hd = 0.639 and π = 0.01073. Further combined sequence analysis revealed a single dominant haplotype (Hap4) representing 56.99% of individuals, indicative of severe haplotype loss and homogenization. Although some haplotypes are shared with wild populations, captive populations exhibit strong genetic differentiation from wild populations, with the captive populations retaining only a limited fraction of the species’ maternal lineages. This pronounced genetic erosion driven by strong founder effects and genetic drift raises concerns about the viability and reintroduction success of this species. These findings highlight the inherent limitations of closed captive populations in preserving evolutionary potential and adaptive capacity. Our study emphasizes the urgent need for evidence-based genetic management, including founder augmentation and population exchange, to mitigate inbreeding and maintain genetic diversity. Full article

Malaria and other haemosporidian parasites are common in reptiles. During baseline health surveys of sea turtles in Western Australia (WA), haemosporidian parasites were detected in flatback (Natator depressus) and green (Chelonia mydas) turtle erythrocytes during routine blood film examination. 130 blood samples were screened via polymerase chain reaction (PCR), including 105 N. depressus, 20 C. mydas, and 5 olive ridley turtles (Lepidochelys olivacea). A novel Haemocystidium sp. was identified, detected exclusively in foraging turtles and not in nesting turtles. The combined prevalence by microscopic and molecular methods was 16.9% (22/130), primarily affecting immature C. mydas (77.3%; 17/22). Mature N. depressus were also affected (22.7%; 5/22). DNA sequencing of a partial fragment of the mitochondrial cytochrome b (cytb) gene together with phylogenetic analysis identified two different Haemocystidium sp. genotypes, A and B, with genotype A being most prevalent. The phylogenetic analysis showed close genetic relationships to Haemocystidium sp. in freshwater and terrestrial turtles, suggesting a shared evolutionary lineage despite ecological differences. Preliminary analysis indicates that this parasite is incidental, as no association between health and parasite presence or grade was detected. This study provides the first formal detection of haemosporidian parasites in sea turtles, contributing essential baseline data while highlighting their evolutionary significance and host–parasite ecological relationships. Full article

Afrotropical regions have high bird diversity, yet few studies have attempted to unravel the prevalence of avian haemosporidia in conservation areas. The diversity and host specificity of parasites in biodiversity hotspots is crucial to understanding parasite distribution and potential disease emergence. We test the hypothesis that biodiverse regions are associated with highly diverse parasites. By targeting the cytochrome b (Cytb) gene, we molecularly screened 1035 blood samples from 55 bird species for avian haemosporidia infections to determine its prevalence and diversity on sites inside and adjacent to the Kruger National Park. Overall infection prevalence was 28.41%. Haemoproteus, Leucocytozoon, and Plasmodium presented prevalences of 17.39%, 9.24%, and 4.64%, respectively. One hundred distinct parasite lineages were detected, of which 56 were new lineages. Haemoproteus also presented the highest diversity compared to Leucocytozoon and Plasmodium with varying levels of specificity. Haemoproteus lineages were found to be specialists while Plasmodium and Leucocytozoon lineages were generalists. We also found a positive relationship between avian host diversity and parasite diversity, supporting an amplification effect. These findings provide insight data for host–parasite and co-evolutionary relationship models. Full article

Rabbit coccidiosis is caused by infection with one or, more commonly, several Eimeria species that parasitize the hepatobiliary ducts or intestinal epithelium of rabbits. Currently, there are eleven internationally recognized species of rabbit coccidia, with the complete mitochondrial (mt) genomes of six species commonly infecting rabbits having been sequenced and annotated. Eimeria kongi was initially discovered in 2011 and prompted a preliminary study on this species. Through traditional morphological analysis, E. kongi was identified as a novel species of rabbit coccidia. To further validate this classification, we sequenced and annotated its mitochondrial genome. The complete mt genome of E. kongi spans 6258 bp and comprises three cytochrome genes (cytb, cox1, cox3), fourteen gene fragments for the large subunit (LSU) rRNA, and nine gene fragments for the small subunit (SSU) rRNA, lacking transfer RNA (tRNA) genes. Moreover, phylogenetic analysis of the mitochondrial genome sequence of E. kongi revealed its clustering with six other species of rabbit coccidia into a monophyletic group. Additionally, E. irresidua and E. flavescens were grouped within the lineage lacking oocyst residuum, consistent with their morphological characteristics. Consistent with multiple molecular phylogenies, in this investigation, E. kongi was further confirmed as a new species of rabbit coccidia. Our research findings are of great significance for the classification of coccidia and for coccidiosis prevention and control in rabbits. Full article

Lions (Panthera leo) play a crucial ecological role in shaping and maintaining fragile ecosystems within Africa. Conservation efforts should focus on genetic variability within wild populations when considering reintroduction attempts. We studied two groups of lions from two conservation sites located in Zambia and Zimbabwe to determine their genetic make-up, information that is usually unknown to the sites. In this study, we analysed 17 specimens for cytb and seven microsatellite markers to ascertain family relationships and genetic diversity previously obtained by observational studies. We then produced a standardised haplogroup phylogeny using all available entire mitogenomes, as well as calculating a revised molecular clock. The modern lion lineage diverged ~151 kya and was divided into two subspecies, both containing three distinct haplogroups. We confirm that Panthera leo persica is not a subspecies, but rather a haplogroup of the northern P.l. leo that exited Africa at least ~31 kya. The progenitor to all lions existed ~1.2 Mya, possibly in SE Africa, and later exited Africa and split into the two cave lion lineages ~175 kya. Species demography is correlated to major climactic events. We now have a detailed phylogeny of lion evolution and an idea of their conservation status given the threat of climate change. Full article

The Neotropical deer genus Mazama is characterized by homoplastic morphological characters, a high karyotypic diversity, and a polyphyletic condition. The species of the genus have been recovered into two multigeneric lineages, the subtribes Odocoileina and Blastocerina, of the tribe Odocoileini (New World deer) in the family Cervidae. Within the Blastocerina, gray brockets include two non-sister species, Subulo gouazoubira, occurring south of the Amazon region, and Passalites nemorivagus, occurring in the Guianas and in the Amazon region. We clarify the taxonomic status and phylogenetic position of Mazama americana citus Osgood, 1912 (referred to as either S. gouazoubira or P. nemorivagus by other authors). We collected a topotype of M. a. citus from the eastern shore of Lake Maracaibo, Venezuela, characterize it morphologically and cytogenetically (conventional banding and fluorescence in situ hybridization), and carry out a phylogenetic analysis of its whole mitogenome and Cytb alongside two additional specimens of M. a. citus from northwestern Venezuela. Our analyses reveal the topotype to be a large gray brocket with a cinnamon band above the eyes and 2n = 61 and FN = 70 karyotype. Using cattle whole chromosome painting and bacterial artificial chromosome X probes, we determined its karyotype to differ in at least 10 rearrangements from that of S. gouazoubira. Bayesian inference recovers M. a. citus within the Blastocerina subtribe, separated phylogenetically from other gray brockets (100% branch value), revealing the Osgood’s gray brocket to be a valid species that should be assigned to a new genus. We propose the generic name Bisbalus, with Bisbalus citus (Osgood, 1912) as the type species. Full article

The joint impacts of historical geological events and Quaternary climatic oscillations in Northwest China on species evolution have been examined extensively in plant under a phylogeographic perspective. However, animal phylogeographic analyses in this region are still limited. The Alashan pit viper, Gloydius cognatus, occurs primarily in arid Northwest China and adjacent areas. Based on variation at two mtDNA genes (ND4 and Cytb) in 27 individuals representing 24 populations, the spatial genetic structure and demographic history of G. cognatus were examined across its geographic range. Phylogenetic analyses revealed two well-supported allopatric clades (each with two distinct subclades/lineages), distributed across the southern (Qaidam Basin, Lanzhou Basin, and Zoige Basin [S1]; Loess Plateau [S2]) and northern (Ily Basin [N1]; Junggar Basin and Mongolian Plateau [N2]) regions. AMOVA analysis demonstrated that over 76% of the observed genetic variation was related to these lineage splits, indicating substantial genetic differentiation among the four lineages. A strong pattern of isolation-by-distance across the sampling populations suggested that geographic distance principally shaped the genetic structure. The four lineages diverged by 0.9–2.2% for the concatenated data, which were estimated to have coalesced ~1.17 million years ago (Mya), suggesting that the expansions of the Badain Jaran, Tengger, and Mu Us deserts during the Xixiabangma glaciation likely interrupted gene flow and triggered the observed divergence in the southern and northern regions. Subsequently, the early Pleistocene integration of the Yellow River and associated deserts expansion promoted the differentiation of S1 and S2 lineages (~0.9 Mya). Both mitochondrial evidence and ecological niche modeling (ENM) reject the signature of demographic and range contractions during the LGM for G. cognatus. In addition, ENM predicts that the suitable habitat of G. cognatus will contract in the future. As such, the conservation and management of ESUs should be a priority. Our findings provide the first insights on the lineage diversification and population dynamics of the Alashan pit viper in relation to geological history and Pleistocene climatic oscillations in arid Northwest China. Full article

Quinquelaophonte is a genus of laophontid harpacticoid, including 13 valid species around the world. Many of them are known to possess inter- and/or intra-individual variations in their swimming legs. During a survey of the meiofaunal biodiversity of Jeju Island in Korea, specimens of Quinquelaophonte were collected from an intertidal zone off the west coast of Jeju Island. This study examined the morphological characteristics and amplified partial sequence of four genes (18S rRNA, 28S rRNA, COX1, and CYTB). As with other Quinquelaophonte species, specimens of this new species showed variability in the chaetotaxy of their swimming legs in both sexes. There was a setal arrangement pattern in females that could be considered a standard, whereas male individuals showed two sets of the chaetotaxy on the fourth swimming legs. The molecular data confirmed that individuals belonged to a single species, regardless of morphological variations. The result of the morphological comparison showed that the new Quinquelaohponte species shared some characteristics with congeneric species but included some specific morphological characters different from its congeners. The new species was named Quinquelaophonte sominer sp. nov. and was presented with detailed descriptions, illustrations, and confocal micrographs. Furthermore, phylogenetic analyses were conducted using newly obtained data plus the sequences of other copepods and two Quinquelaophonte species. The result suggested that Q. sominer sp. nov. and two congeners were classified as branched lineages. This discovery brings the total number of species to three in the Northwest Pacific region. Full article

A range-wide phylogenetic/phylogeographic study of the three-toed jerboas of the genus Stylodipus is conducted using the mitochondrial cytb gene and fragments of several nuclear genes. The genus has been believed to include three species: S. telum (W Central Asia, SE Europe), S. andrewsi (E Central Asia), and S. sungorus (Dzungar basin). Our data support the dichotomy between S. andrewsi and the other taxa forming S. telum species group. Within the latter, both mtDNA and nuclear loci indicate a species-level divergence between S. telum and the S. t. birulae lineage (Zaisan depression, NE Kazakhstan), previously considered a subspecies of S. telum and here elevated to full species. S. sungorus is recovered as a close sister group to S. birulae on the basis of nuclear data but clustered with S. telum in the mitochondrial tree. The latter taxon is the most variable and includes two closely related eastern and western sublineages, separated by the Volga-Ural sands and joined by a more divergent S. t. karelini lineage (E Kazakhstan). The observed mitonuclear discordance is hypothesized to occur due to mtDNA introgression resulting from hybridization between S. sungorus and S. t. karelini, which highlights the important role of reticulations in the evolution of Dipodidae. Full article

Environmental DNA (eDNA) analysis is a biological survey method that has drawn much attention in recent years. However, the results of eDNA analysis and capture surveys often do not completely match, and the validity of the eDNA analysis needs to be verified. Verification of eDNA metabarcoding was conducted in a river in Fukushima Prefecture, Japan, in comparison with capture survey data. Most of the captured species were detected, and 13 uncaptured lineages (two genera and 11 species) were detected in the eDNAs. Some rare species detected in the eDNAs were also identified, including exotic eels and an endangered yet out-of-range bitterling fish. To confirm the validity of the exotic Anguilla spp. detected in eDNAs, mitochondrial Cytb sequencing was performed on captured eel specimens. All eel specimens were sequenced as the native Anguilla japonica, indicating a small biomass of the exotic species difficult to capture. Our results clearly indicated the eDNA analysis as a powerful tool for detecting possible habitats of rare fish species without disturbance to the natural environment. Full article

The Military Macaw (Ara militaris) is an endangered bird species with disjunct geographic distribution across the Neotropics, consisting of three recognized subspecies: One in Mexico (A. m. mexicanus) and two in South America (A. m. militaris and A. m. bolivianus). However, due to the limited phenotypic differentiation between these allopatric taxa, their taxonomic status has been the subject of debate. In this study, we explored mitochondrial DNA (mtDNA) variability to determine the phylogeographical pattern through phylogenetic and ecological modelling analyses. We also aimed to describe the evolutionary relationships of twelve A. militaris populations. We identified 41 haplotypes in the 300 bp region of the Cytochrome b (Cyt-b) gene of the mtDNA and low nucleotide diversity. The observed phylogeographic structure suggests the existence of two clades: One composed of A. m. militaris and A. m. bolivianus and another consisting solely of A. m. mexicanus. The A. m. mexicanus clade further divides into two recognized subclades: Sierra Madre Oriental and northeastern portion of the Sierra Madre Occidental. Ecological analyses revealed that the niche similarity between these lineages was lower than expected by chance. Additionally, results from low cross-prediction tests indicated that the two lineages have inhabited different environmental spaces since the Late Pleistocene. This divergence may be associated with a steep ecological gradient and contemporary geographical barrier. Based on our results, we suggest that at least the A. m. mexicanus has a divergent evolutionary history; therefore, it should be considered as a different evolutionarily significant and management unit. We recommend that future conservation strategies in Mexico incorporate effective protection measures, including habitat preservation and the reduction of illegal trade, to ensure the preservation of viable populations. Full article