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Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change. [ABSTRACT FROM AUTHOR]

We sequenced the complete mitochondrial genome of the aphid Periphyllus koelreuteriae. It is 16,828 bp long and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosome RNA genes (rRNAs), a control region, and a repeat region. The control region contains a 273-bp repeat motif repeated 2.3 times. The species-specific repeat region between trnE and trnF comprises two 340-bp repeat units. The maximum-likelihood tree based on all 37 mitochondrial genes indicated a close relationship between P. koelreuteriae and Periphyllus diacerivorus. This study provides a valuable mitogenomic resource for future research on Chaitophorinae phylogeny and P. koelreuteriae diversification. [ABSTRACT FROM AUTHOR]

Genetic connectivity and historical population expansion are characteristics that have largely been studied and observed in several members of the Lutjanidae family throughout the Western South Atlantic, particularly in Brazilian waters. In this study, the population genetic structure of Lutjanus jocu was investigated using four genomic regions: two from mitochondrial DNA (Control Region and Cytochrome B) and two nuclear genes (Delta 6 desaturase—intron 8 and Ribosomal Protein S7—intron 1), in 144 specimens distributed in six locations on the Atlantic coast of Brazil. The results revealed high levels of genetic diversity for both mtDNA and nuDNA markers, and intense gene flow, indicating, consistent with other studies, that this species is represented by a single genetic stock along the Brazilian coast. This is likely due to the high dispersal capacity of L. jocu larvae, driven by the main equatorial currents, as well as biological and ecological factors, contributing to a genetically homogeneous population. Historical demographic analysis and neutrality tests suggest that the species experienced population expansion, possibly during the Pleistocene. Information regarding the genetic structure of populations is extremely important, especially for species of high economic and fishing importance, and can be very useful in guiding stock management and management measures. [ABSTRACT FROM AUTHOR]

We sequenced the complete mitochondrial genome of the aphid Periphyllus koelreuteriae. It is 16,828 bp long and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosome RNA genes (rRNAs), a control region, and a repeat region. The control region contains a 273-bp repeat motif repeated 2.3 times. The species-specific repeat region between trnE and trnF comprises two 340-bp repeat units. The maximum-likelihood tree based on all 37 mitochondrial genes indicated a close relationship between P. koelreuteriae and Periphyllus diacerivorus. This study provides a valuable mitogenomic resource for future research on Chaitophorinae phylogeny and P. koelreuteriae diversification.

The yellowtail snapper Ocyurus chrysurus Bloch, 1791 (Perciformes: Lutjanidae) is targeted by recreational or commercial fisheries across much of its range in the western Atlantic Ocean, from Massachusetts, USA, to São Paulo, Brazil. Genomic resources to support conservation of this species are needed. Here, we assembled, annotated and characterised in detail the mitochondrial genome of O. chrysurus. The mitochondrial genome of O. chrysurus is 16,502 bp in length and encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). The putative control region, 827 bp in length, is located between the tRNA P and tRNA F genes. Most genes are encoded on the positive strand, while a single PCG (nad6) and six tRNA genes (in order from 5′ to 3′: tRNA N, tRNA P, tRNA E, tRNA Q, tRNA C and tRNA Y) are encoded on the negative strand. All tRNA have a typical 'cloverleaf' secondary structure except tRNA S1 (Serine1) that lacks the D arm. Calculated Ka/Ks values of all PCGs were <1, suggesting that these genes are under purifying selection. A maximum likelihood (ML) phylogenetic analysis confirmed monophyly of the family Lutjanidae and indicated that the genus Lutjanus is paraphyletic given that O. chrysurus clustered together with Lutjanus peru and L. guttatus in a strongly supported clade. Data published herein will inform conservation and management strategies for this fished snapper. [ABSTRACT FROM AUTHOR]

The Pearl darter Percina aurora, a member of the species-rich family Percidae, is endemic to the Pearl and Pascagoula river systems in Louisiana and Mississippi, USA. However, this fish is now only found in the Pascagoula River and is listed as threatened under the US Endangered Species Act. This study, for the first time, assembled and characterised in detail the mitochondrial genome of P. aurora. The mitochondrial genome of P. aurora is 16,646 bp in length and comprises 13 protein coding genes (PCGs), 22 transfer RNA genes, and 2 ribosomal RNA genes (rrnS [12s ribosomal RNA] and rrnL [16s ribosomal RNA]). A 33 bp long region was identified as the origin of replication for the light strand (OL), and a putative non-coding control region (CR), 987 bp in length, contains the origin of replication for the heavy strand (OH). The two ribosomal RNA genes, the majority of the PCGs, and the majority of the tRNA genes are encoded on the positive, or heavy, strand. The gene order in P. aurora is identical to that previously reported for confamilial species. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 which lacked the D-arm loop. An analysis of selective pressure (Ka/Ks ratios) for all the PCGs showed Ka/Ks values ≤1, suggesting that all these PCGs experience strong purifying selection. This new genomic resource will aid with bioprospecting and biomonitoring of P. aurora using environmental DNA. [ABSTRACT FROM AUTHOR]

The marbled flounder (Pseudopleuronectes yokohamae) is a demersal flatfish species, widely distributed in the northwestern Pacific region. In the present study, the mitochondrial DNA (mtDNA) control region was used to determine the genetic diversity and population genetic structure of this species. We obtained a 380 bp segment of the mtDNA control region after the alignment of 78 individual sequences from P. yokohamae collected from two locations in Korea (Biungdo and Mukho) and one location in Japan (Tohoku) and 103 individual sequences from a previous study (Yokjido and Namhae). The overall haplotype diversity and nucleotide diversity were 0.983 ± 0.003 and 0.016 ± 0.008, respectively. The genealogical relationships of the mtDNA control region did not exhibit any specific genealogical association according to sampling location. The pairwise FST value indicated that the Biungdo (west coast of Korea) and Tohoku (Japan) populations showed genetically differentiated structures (but the Tohoku and Mukho populations did not). However, there was no discernible difference between the Mukho population from Korea's eastern coast and the Yokjido and Namhae populations from the southern coast. The biological characteristics of P. yokohamae and oceanographic barriers may have contributed to producing genetically distinct populations. [ABSTRACT FROM AUTHOR]

The population of the Northwest Pre-Caspian saiga (Saiga tatarica tatarica) numbered about 800 000 individuals in the middle of the last century. There was a dramatic decline at the end of the 20th century, and by 2015 the numbers of this saiga population reached about five thousand animals. The results of microsatellite loci and of mtDNA control region analysis obtained for museum saiga samples from the Northwest Pre-Caspian population, collected at the peak of their numbers in the 1950s, are presented. We compared these data with our previous results for the samples collected during the population depression in the years 1999–2016. There were no noticeable differences in the mtDNA control region diversity between the museum and modern saiga samples. The most vivid genetic consequence of the severe decline in population numbers was a significant increase of the inbreeding coefficient (Fis) calculated from the microsatellite loci. [ABSTRACT FROM AUTHOR]

Background: The genus Corynorhinus is composed of four recognized species: C. rafinesquii, C. townsendii, C. mexicanus, and C. leonpaniaguae, the latter two being endemic to Mexico. According to the IUCN, C. mexicanus is considered "Near Threatened", as its populations are dwindling and habitats are affected by anthropogenic disturbance. Corynorhinus leonpaniaguae has not been assigned to an IUCN Red List risk category due to its recent description. Methods and results: In this study, the mitochondrial genomes of C. mexicanus and C. leonpaniaguae were assembled and characterized in detail. The mitochondrial genomes (mtDNA) of C. mexicanus and C. leonpaniaguae have lengths of 16,470 and 16,581 bp respectively, with a predominant nucleotide usage of adenine (31.670% and 31.729%, respectively) and thymine (26.15% and 26.18%, respectively). The mtDNA of C. mexicanus and C. leonpaniaguae is composed of 37 coding and non-coding elements: 22 transfer RNAs (tRNA), 13 protein-coding genes (PCGs), two ribosomal RNAs and a non-coding region, the control region, which has a length of 933 bp and 1,149 bp, respectively. All tRNAs exhibited a cloverleaf secondary structure, with the exception of trn-Ser1 which showed a deletion of the dihydrouridine arm in the two species. All PCGs are subjected to purifying selection, with atp8 being the gene showing the highest Ka/Ks value. Conclusions: These are the first whole mitogenomic resources developed for C. mexicanus and C. leonpaniaguae and enhance our knowledge of the ecology of these species and aid in their conservation. [ABSTRACT FROM AUTHOR]

We present here the complete mitochondrial sequence of the critically endangered Malaysian giant turtle, Orlitia borneensis. The assembled mitochondrial genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (rRNAs), and one control region. This mitochondrial genome has been archived in the NCBI GenBank with accession number OQ808845. The Batagur control region is relatively smaller than O. borneensis and closer to Aldabrachelys gigantea, which suggests potentially that O. borneensis has undergone an expansion in the control region. [ABSTRACT FROM AUTHOR]

Gallus varius, an indigenous bird species of Indonesia, demonstrates significant genetic diversity. The genetic diversity assessment in G. varius encompassed both mitochondrial DNA (mtDNA) and nuclear DNA, with the mtDNA analysis primarily centered on domain I of the control region. This study aimed to describe the genetic diversity and structure of G. varius inhabiting Java, Madura, Lombok and Sumbawa based on the middle-lower part of control region mtDNA. Genomic DNA was extracted from the calamus tip of feather, then the middlelower part of control region was amplified and sequenced using two pairs of primers. In the examined control region, spanning from 944 to 1,008 bp, 13 bp of nucleotide variation was observed, with nucleotide diversity at 0.0021. Between G. varius samples and the reference (NC_007238.1), a total of 7 haplotypes were identified, 5 unique and 2 shared haplotypes, with haplotype diversity at 0.7692. The substantial diversity of haplotypes in this study and two previous study suggests that the genetic diversity of G. varius has remained stable over the past two decades. Additionally, genetic distance data indicate there is multiple G. varius subspecies, and the haplotype network accentuates signs of population differentiation. [ABSTRACT FROM AUTHOR]

The Asian monsoon scallop, Amusium pleuronectes, is a key member of the most commercially harvested shellfish community in Asia. Patterns of genetic diversity and natural population structure in the target species were investigated to gain a better understanding of its evolutionary history. Samples were collected from five sites across the Indonesian Archipelago. We characterized sequence variation in an mtDNA control region fragment in 249 individuals. The genetic diversity (h = ranging from 0.83 to 0.92) and nucleotide diversity (π = ranging from 0.24 to 0.32) were low compared to the estimates reported for many other similar shellfish taxa. Nonetheless, analysis of molecular variance revealed significant genetic differentiation, FST = 0.0203 (p <.005 after Bonferroni corrections). Furthermore, both Pairwise fixation index values showed significance among majority population sites, indicating that dispersal potential and gene flow were low in the past. This pattern likely reflects a low dispersal potential, potentially allowing local adaptation to sites that augment any oceanographic and geographic contribution to genetic structure. The results described herein provide a foundation for developing better conservation strategies for the target species in the future. [ABSTRACT FROM AUTHOR]

Here we report the first thorough genetic characterization of the long-understudied red deer population of Belarus in regards to its ancestry according to mtDNA sequence analysis. Employing a 346 base pair segment of the mitochondrial control region (d-loop) from 36 deer specimens of either sex recently harvested across the country, we have discovered 10 haplotypes belonging to 3 of the widely described European red deer lineages, or haplogroups: Iberian (A), Tyrrhenian (B), and Maraloid (E), clarifying the range limits of those lineages in the region. Combining this data with a comparative analysis of genetic diversity and historical records, we conclude that the Belarusian population of red deer has an artificially mixed origin, though it remains unclear how desirable such a state is, in terms of sustainable management, use, and conservation. Inquiries into ancient DNA are required to recognize the lineages closest to the autochthonous deer population of Belarus. [ABSTRACT FROM AUTHOR]

In this study, Little Tern (Sternula albifrons) populations in Taiwan are examined based on two different types of data: mitochondrial control region DNA sequences and double digest restriction-site associated DNA (ddRAD) sequencing data. Feather samples were collected from 59 chicks across four known breeding colonies located on the eastern (Yilan and Hualien) and western (Penghu and Changhua) coasts of Taiwan. The results obtained are consistent in analyses and do not cluster into two geographical groups with respect to the eastern and western Taiwan. Furthermore, AMOVA analyses and pairwise ΦST/FST estimations based on both types of data reveal little to no differentiation among populations and between groups. The findings of this study suggest high population connectivity among Taiwan's breeding colonies. Additionally, control region sequences of Taiwan's Little Terns are compiled with those from Japan deposited in GenBank to compare genetic diversity and examine for phylogeographic breaks that could shape the diversity pattern of the species in eastern Asia. The resulting haplotype network does not clearly separate Taiwanese and Japanese populations, but the three most common haplotypes are prevalent for mainland Japan, Okinawa, and Taiwan. Little Tern populations may be frequently connected, but with some restrictions on gene flow causing moderate to great differentiation among the three. This is further supported by AMOVA analyses, pairwise ΦST estimations, and pattern of positive yet significant isolation by distance. [ABSTRACT FROM AUTHOR]

Schreiber’s bent-winged bat Miniopterus schreibersii (Chiroptera) is a widespread, cave-dwelling, regionally migrating species whose genetic diversity was studied throughout its distribution area using mitochondrial and nuclear markers. Previous studies revealed little to no structuring of populations and established Anatolia to be a single refugium during the last glacial maximum. The Balkans were well covered in these studies but usually lacked samples from Serbia. We sequenced the mitochondrial hypervariable region 1 (HV1) gene in M. schreibersii collected at seven sites in Serbia to assess their genetic relatedness to other European and Asia Minor populations and check whether the Balkans exhibit a higher genetic diversity than Western Europe due to its closeness to Anatolia. We recorded nine haplotypes from Serbia, six of which had not been previously reported, with a haplotype diversity of 0.585. The remaining three were shared with individuals from Portugal, Greece, and Turkey. A single most common haplotype was present throughout the species distribution range, pointing to a well-connected population and as indicated by the shape of the haplotype network, a common origin, and a sudden population expansion. Results complement existing data on M. schreibersii having a non-structured population, adding valuable new data from the Balkans supporting the previous hypothesis about its Anatolian origin.

Abstract Background Even though the Buyei are a recognised ethnic group in southwestern China, there hasn’t been much work done on forensic population genetics, notably using mitochondrial DNA. The sequences and haplogroups of mitochondrial DNA control regions of the Buyei peoples were studied to provide support for the establishment of a reference database for forensic DNA analysis in East Asia. Methods and results The mitochondrial DNA control region sequences of 200 Buyei individuals in Guizhou were investigated. The haplotype frequencies and haplogroup distribution of the Buyei nationality in Guizhou were calculated. At the same time, the paired Fst values of the study population and other populations around the world were computed, to explore their genetic polymorphism and population relationship. A total of 179 haplotypes were detected in the Buyei population, with frequencies of 0.005–0.015. All haplotypes were assigned to 89 different haplogroups. The haplotype diversity and random matching probability were 0.999283 and 0.0063, respectively. The paired Fst genetic distances and correlation p-values among the 54 populations revealed that the Guizhou Buyei was most closely related to the Henan Han and the Guizhou Miao, and closer to the Hazara population in Pakistan and the Chiang Mai population. Conclusions The study of mitochondrial DNA based on the maternal genetic structure of the Buyei nationality in Guizhou will benefit the establishment of an East Asian forensic DNA reference database and provide a reference for anthropological research in the future.

The southern three-banded armadillo, Tolypeutes matacus , is one of the most representative species of the South American Chaco region. The susceptibility of this species to climatic changes and its good number of paleontological records has led to the study of their range dynamics for untangling the effects of Quaternary oscillations. These studies yielded contradictory results, suggesting expansion processes under opposite conditions: some during glacial periods and others during interglacial periods. Here, we assess the population structure of T. matacus in Argentina based on mitochondrial genes, and estimate demographic and spatial dynamics that contribute to unveiling the evolutionary process that moulded its biogeography. We found no clear phylogeographical breaks, although there were differences in the composition and frequency of haplotypes between the northern and southern localities studied. Demographic inferences indicate that the species has undergone population and range expansion processes. The higher diversity found in the north and the spatial diffusion analysis allow us to infer a north–south direction of this expansive process. Our results yield essential evidence for disentangling the evolution of this Chacoan species linked with Quaternary climates and provide genetic information about its populations that should be taken into account for the conservation of this threatened mammal. [ABSTRACT FROM AUTHOR]

Simple Summary: The tundra vole's (Alexandromys oeconomus) distribution in Lithuania has been documented for 70 years, yet its genetic diversity remains unexplored. We analyzed vole samples from northern and western sites in Lithuania, using mtDNA sequence analysis. Despite landscape barriers, our phylogenetic analyses placed Lithuanian voles in the Central European phylogroup, suggesting an origin from northeastern Poland. Genetic diversity in Lithuanian A. oeconomus at the mtDNA loci was low compared to other European samples, revealing distinctions from Poland and Northern Europe. Genetic divergence among western and northern Lithuanian samples, coupled with low variability, provides novel insights into species phylogeography and the influence of barriers on colonization dynamics. The distribution and spread of the tundra vole (Alexandromys oeconomus) in Lithuania have been documented over the last 70 years, but the genetic diversity of the species has not been studied. In this study, we examined A. oeconomus trapped in three sites in northern and western Lithuania using mtDNA sequence analysis of the cytb and control region. The western and northern sites are separated by anthropogenic landscape barriers. The western site is subject to regular spring flooding. Phylogenetic analyses of the studied individuals placed them in the Central European phylogroup, suggesting that Lithuanian A. oeconomus originated from northeastern Poland. In Lithuania, the genetic diversity of A. oeconomus at both mtDNA loci was relatively low (Hd < 0.6, π < 0.002) compared to that found in other European samples (Hd = 0.833–0.958; π = 0.00402–0.01552). Individuals analyzed in Lithuania were genetically different from samples collected in Poland and Northern Europe (ΦST > 0.15, p < 0.05). The genetic divergence between the western and northern samples of A. oeconomus in Lithuania, together with the low genetic variability among the voles studied, provides new insights into the phylogeography of the species and the influence of barriers on the colonization of the country. [ABSTRACT FROM AUTHOR]

The Yellowspotted Puffer Torquigener flavimaculosus (Hardy & Randall, 1983) invaded the Mediterranean from the Red Sea via the Suez Canal. In the present study, we analyzed two mitochondrial loci, the cytochrome c oxidase 1 (COI) and the control region (D-loop), from the Mediterranean and the Red Sea populations. Both the COI and the D-loop showed no decrease of genetic variability in the Mediterranean population compared to the source population from the Red Sea. When comparing the genetic variability to two other species of the Tetraodontidae family (Takifugu rubripes and Takifugu obscurus), the mean divergence within the T. flavimaculosus is almost twice as large. T. flavimaculosus has two distinct genetic groups, similarly represented both in the Red Sea and in the Mediterranean, with similar coefficients of differentiation in COI, in D-loop, and, not surprisingly, in the two genes combined. This suggests that T. flavimaculosus has most likely established a sustainable population in the Suez Canal, that has gradually dispersed northward and eventually entered the Mediterranean with a large number of individuals, carrying a great deal of its genetic variability. [ABSTRACT FROM AUTHOR]

Three endemic and threatened lizards of the genus Pristidactylus inhabit in central Chile, which have very limited distributions. Mitochondrial (cytochrome b) genetic variation was examined in two populations of each of these three species. The analyses suggest that they have large population sizes, high population structure and low gene flow between their populations. The implications of these results for the conservation of these species are discussed.

The highly migratory and marine nature of species such as green sea turtles (Chelonia mydas) may hinder understanding of basic life history and impact ensuing management and conservation applications across their full range. To elucidate the linkages between juvenile green turtles foraging in coastal waters of Uruguay in the Southwestern Atlantic Ocean to their future nesting or feeding grounds, this study investigated their genetic composition . A total of 201 tissue samples were collected from turtles that had stranded or were intentionally captured for scientific research along the Uruguayan coast (ca. 33°–35°S) during two sampling periods (2003–2005 and 2009–2014). Samples were pooled for analysis. Twelve mitochondrial control region haplotypes and ten subhaplotypes were identified, all of which had been previously detected at Atlantic or Caribbean nesting beaches. Mixed Stock Analysis revealed that most turtles traced to the Ascension Island rookery, representing a substantial connection to the remote mid-Atlantic island thousands of kilometers distant. Other nesting areas, such as Guinea Bissau in Africa and Trindade Island in Brazil, represented less significant sources. There was no significant temporal or spatial genetic structure within Uruguayan waters, suggesting dispersion along this coast. Despite the geographic distance from the nesting beach, the significant connection to the Ascension Island rookery underscores the importance of considering rookery population size and ocean current influences in understanding source contributions. These findings emphasize the need for conservation efforts, including the maintenance of existing protected areas and the creation of new ones, to ensure the long-term conservation of green turtles connected to various nesting colonies and feeding grounds.

Abstract Background As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. Results To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. Conclusions In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.

The marbled flounder (Pseudopleuronectes yokohamae) is a demersal flatfish species, widely distributed in the northwestern Pacific region. In the present study, the mitochondrial DNA (mtDNA) control region was used to determine the genetic diversity and population genetic structure of this species. We obtained a 380 bp segment of the mtDNA control region after the alignment of 78 individual sequences from P. yokohamae collected from two locations in Korea (Biungdo and Mukho) and one location in Japan (Tohoku) and 103 individual sequences from a previous study (Yokjido and Namhae). The overall haplotype diversity and nucleotide diversity were 0.983 ± 0.003 and 0.016 ± 0.008, respectively. The genealogical relationships of the mtDNA control region did not exhibit any specific genealogical association according to sampling location. The pairwise FST value indicated that the Biungdo (west coast of Korea) and Tohoku (Japan) populations showed genetically differentiated structures (but the Tohoku and Mukho populations did not). However, there was no discernible difference between the Mukho population from Korea’s eastern coast and the Yokjido and Namhae populations from the southern coast. The biological characteristics of P. yokohamae and oceanographic barriers may have contributed to producing genetically distinct populations.

Mitochondrial DNA (mtDNA) analysis has proven to be an excellent tool for studying the genetic ancestry of many populations. It is also helpful for forensic investigations because of its unique qualities, such as a high mutation rate, maternal mode of inheritance, a high quantity of copies in cells, and control region with specific genetic markers. Therefore, the present study is conducted to establish high-quality forensic data, as well as to assign predominant haplogroups by studying variations generated from mitochondrial DNA control regions among the south Indian Muslims. To this aim, 5ml blood samples were collected from 60 healthy unrelated Muslim individuals of Srirangapatna town in Karnataka state, South India. DNA extracted from the blood sample was amplified, and the sequence of the control region of mtDNA was determined by the Sanger method. Using these sequence data, 48 different haplotypes and 113 polymorphic positions were defined. Of the 48 haplotypes assessed, 40 were unique, and eight were observed in more than one individual. Diversity indices such as genetic diversity, power of discrimination, and random match probability were 0.9870, 0.9705, and 0.0294, respectively. The mean of pairwise differences was estimated at 14.671751 +/- 6.659951 and nucleotide diversity at 0.019229 +/- 0.009680. Consequently, the low random match probability and high genetic diversity were obtained from the present data, while previous studies suggest a high heterogeneity in the Indian Muslim population. The haplogroup pattern and its frequency were indicative of the composition of South Asian (52%), West Eurasian (28%), and West Asian (20%) genetic content in this population. The diversity indices and phylogenetic findings confirm the high potential of mtDNA control region polymorphisms in forensic investigation casework and phylogenetic studies.

We analyzed population genetic structure of polar bear (Ursus maritimus) in the Russian Arctic based on samples collected in 2010–2021. For 93 adult individuals, we report polymorphism of 17 nuclear DNA microsatellite loci and a 610 nucleotide long mtDNA D-loop fragment. High genetic diversity of nuclear DNA and low nucleotide diversity π for mitochondrial DNA was found. All genetic markers proved differentiation between bears of southern Barents Sea and northern Barents and Kara seas. These two groups differed by distribution of the mitochondrial marker (θst = 0.270) and, to less extent, by nuclear loci (Rst = 0.018). [ABSTRACT FROM AUTHOR]

Background: As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. Results: To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. Conclusions: In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion. [ABSTRACT FROM AUTHOR]

Introduction: The rough-toothed dolphin (Steno bredanensis) inhabits oceanic waters of tropical latitudes and exhibits philopatry in some oceanic islands. However, the species has been observed in shallow coastal waters in a few areas. Particularly in Central America, the rough-toothed dolphin has been reported by occasional records and strandings. For instance, the first confirmed record of this species in the Panama's Caribbean was on July 17, 2012, in a coastal region of the Chiriquí Lagoon during a bottlenose dolphin monitoring survey. Similarly, the first rough-toothed dolphin mass stranding reported for the Pacific of Panama was on April 20, 2016, at the Ostional Beach, where 60 dolphins stranded and ten died. These sightings and events offered a valuable opportunity to obtain samples to conduct genetic studies, which are scarce in the region. Objective: In this study, we present the first assessment of genetic diversity for rough-toothed dolphins based on mitochondrial DNA Control Region (mtDNA-CR) in the Panamanian Pacific and the Wider Caribbean. Methods: Samples were collected in Colombia (N=5), Panama (N-Caribbean=1, N-Pacific=9), and Puerto Rico (N=3) from free-ranging and stranded individuals. DNA was extracted from each sample, and a mtDNA segment of around 534 to 748 bp was amplified through the PCR reaction. The obtained sequences were compared with rough-toothed dolphin haplotypes previously published in NCBI (N=70), from the Atlantic, Indian, and the Pacific Oceans. Results: Our findings showed significant population structure among ocean basins (strong differentiation with ΦST data), and high genetic diversity within each phylogroup. Only the Atlantic Ocean showed high genetic differentiation within the basin, detecting three phylogroups: the Caribbean, northern, and southern Atlantic. Conclusions: These findings support previous genetic studies that indicate high levels of population structure among ocean basins, although this species seems to be widely dispersed. However, samples from Panama and the Caribbean appear to show connectivity between highly differentiated Atlantic and Pacific Oceans. Therefore, our results highlight the need for more research to assess the rough-toothed dolphin genetic and population status in Central America, as the piece of the puzzle needed to clarify its taxonomy and genetic differentiation worldwide. This information is needed due to the rough-toothed dolphin IUCN categorization as "Least Concern" and its classification into appendix II according to CITES. While individuals are potentially threatened by incidental fishing, no management units are currently used to conserve this species despite its high genetic differentiation. [ABSTRACT FROM AUTHOR]

Generally, a teleostean group (e.g., family or genus) owns one type or a set of similar mitochondrial gene arrangement. It is interesting, however, that four different types of gene arrangement have been found in the mitochondrial genome (mitogenome) of Cynoglossidae species. So far, the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of controversy. Here, a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes (Pleuronectiformes: Cynoglossidae) were compared. The length ranges from 16 417 bp to 18 369 bp, which is mainly caused by the length heteroplasmy of control region (CR). Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length heterogeneity. Like most gene rearrangements of Cynoglossinae mitogenomes, tRNA-Gln gene encoded by the L-strand has translocated to the H-strand (Q inversion), accompanied by the translocation of CR in C. puncticpes mitogenome. The typical IQM order (tRNA-Ile-Gln-Met) changed to QIM order. Tandem duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in C. puncticpes mitogenome. Phylogenetic trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny, which provides a fresh idea for phylogenetic studies in future. [ABSTRACT FROM AUTHOR]

Context. Investigating the patterns of genetic diversity and population structure of the Javanese ricefish, Oryzias javanicus, is instrumental in identifying their dispersal patterns and demographics in response to ecological changes and biogeographical barriers. Aims. To acquire a better understanding of the evolutionary history of Javanese ricefish. Methods. We sequenced part of the mitochondrial DNA (mtDNA) control region in 335 individuals and genotyped 280 individuals for four microsatellite loci from seven Indonesian sites. Key results. Both genetic diversity (h = 0.19-0.86 and DIVGene = 0.10-0.43) and nucleotide diversity (π = 0.06-0.61%) were low compared with other fish taxa. The analysis of molecular variance showed considerable genetic differences (P < 0.0001) for both genetic markers across all sampled locations. These results suggest that there has been a historical restriction on gene flow. Conclusion. The observed population-structure pattern reflects a short pelagic larval development, which is closely linked to a restricted dispersal potential. This ultimately leads to isolation by distance, potentially allowing local adaptation to sites that augment any oceanographic, geographic, or biological barriers to gene flow. Implications. The results presented in this study can be used to create more effective ways to protect the species in question. [ABSTRACT FROM AUTHOR]

The tufted deer (Elaphodus cephalophus) is a unique species in the genus Elaphodus. Currently, very little is known about its nuclear and mitochondrial genomes and their phylogenetic position within the family Cervidae. In this study, we have determined the complete sequence of the mitochondrial genome of the tufted deer, by using a long polymerase chain reaction (PCR) technique. The entire mtDNA sequence is 16,196 bp in length, which compared with previous studies is the least, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (CR, D-loop). The overall base composition included 33.37 % A, 29.33 % T, 23.94 % C, and 13.36 % G. According to 13 protein-coding genes and phylogenetic analysis, Elaphodus may have a sister relationship with another deer group Muntiacus and they belong to the monophyletic genus. This study depicted mitochondrial genome characteristics for E. cephalophus and deepened the understanding of the phylogenetic relationship of Cervidae. [ABSTRACT FROM AUTHOR]

The brushtooth lizardfish, Saurida undosquamis (Richardson, 1848), is a valuable warm-water bottom fish with medicinal and economic value. This study utilized mitochondrial DNA cytochrome b (Cytb) and control region (CR) sequences to study the genetic diversity, population structure, and historical dynamics of four S. undosquamis populations in the South China Sea. Results showed that the alignment length of Cytb was 892 bp and that of the CR was 969 bp. In total, 59 polymorphic loci were detected in Cytb, defining 58 haplotypes. The overall haplotype and nucleotide diversity of the four populations were 0.9497 and 0.0041, respectively, and 104 polymorphic loci were detected in the CR, defining 97 haplotypes. The overall haplotype and nucleotide diversity of the four populations were 0.9980 and 0.0109, respectively. The haplotype phylogenetic tree, haplotype network diagram, and genetic differentiation index revealed no significant genetic differences among the four S. undosquamis populations. The results of the neutral test and mismatch analysis indicated that S. undosquamis expanded between 30.1 and 55.4 thousand years ago. The genetic diversity indicators obtained in this study will serve as basic data for future mitochondrial DNA polymorphism monitoring and research on S. undosquamis fishery resources.

Simple Summary: The artisanal octopus fishery is a great tradition and has a large economic impact in Northern Spain. Despite its importance, there is scarce genetic information for this exploited population. The uniqueness of an exploited population and the effects that exploitation may have on its long-term survival is essential information that can be obtained by studying the past and current spatial and temporal genetic patterns. The mitochondrial DNA is used here as a genetic tool to gain insight into Northeast Atlantic octopus populations and their evolutionary history. Although it is not sensitive enough to detect differences in nearby populations, it allows us to differentiate the two main lineages that originated during the Quaternary glaciations. One of the lineages is present exclusively in northern latitudes and the other mainly in the south, although, for the first time, its presence is demonstrated also in the north of the Iberian Peninsula. This implies a more continuous distribution than previously thought for this lineage. We also detect temporal changes in the distribution of the two lineages in contact zones. These changes seem to be associated with the effect of changing oceanographic conditions. Future studies on these associations could be of interest for fisheries in the scenario of global climate change. Octopus vulgaris is one of the most harvested octopus species in the world. In the Iberian Peninsula, there are several small-scale fisheries that have a long-term tradition of harvesting octopus. The Asturias fleet (in Northern Spain) has an internationally recognized MSC label for its exploitation. Of concern, genetic assessments of exploited stocks are currently scarce, which could prevent the implementation of adequate managing strategies. We use two mitochondrial regions (cytochrome oxidase subunit 1 and control region) to analyze the genetic status and evolutionary events that conditioned octopus populations' characteristics in the Northeastern Atlantic. A total of 90 individuals were sampled from three different localities in the Iberian Peninsula as well as a location in Macaronesia. Temporal genetic analyses on Asturias and Algarve populations were also performed. Results indicated the absence of fine spatial genetic structuring but showed the Canary Islands (in Macaronesia) as the most distinct population. Our analyses detected two distinct clades, already described in the literature, but, for the first time, we confirmed the presence of the α-southern haplogroup in the Northern Iberian Peninsula. This result indicates a more continuous cline for the distribution of these two haplogroups than previously reported. Temporal changes in the distribution of both haplogroups in contact zones were also detected. [ABSTRACT FROM AUTHOR]

Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero & Ramírez, 2023 and Pomacea aulanieri (Deville & Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri—which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea. [ABSTRACT FROM AUTHOR]

Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae. [ABSTRACT FROM AUTHOR]

Brown croaker (Miichthys miiuy), a species of fish with significant commercial value, is found in the coastal seas of Korea, China, and Japan. The genetic diversity and population structure of a representative sample of brown croaker specimens were assessed based on the control region of their mitochondrial DNA (mtDNA). Samples from a total of 115 individuals were collected from three separate locations, one in China (Lianyungang) and two in Korea (Mokpo and Gyeongnyeolbiyeoldo Island). Analysis of the 436-base-pair mtDNA control region revealed that the haplotype diversity ranged from 0.973 ± 0.025 to 0.988 ± 0.008, while the nucleotide diversity ranged from 0.012 ± 0.006 to 0.017 ± 0.009. The level of genetic diversity, star-shaped haplotype network, significant Fu's Fs test, and analysis of the mismatch distribution all suggested that this species has experienced population expansion. Fixation index analysis indicated that the population collected at the site in China differed significantly from the two populations obtained in Korea. The findings of this study extend the general understanding of the population structure of M. miiuy and can be used to develop strategies for effective resource management. [ABSTRACT FROM AUTHOR]

In this study, we examined the mitochondrial DNA diversity of Eurasian otter from European Russia and Transcaucasian countries and compared it with other European populations. We used a fragment of the mtDNA control region (255 bp) and also included previously detected haplotypes from NCBI. Six haplotypes were found in 75 samples from European Russia and Transcaucasian countries. Lut1 was the most common haplotype (62.1% of samples); Lut4 was detected in 17.6% of samples; the other four haplotypes were newly detected. Haplotype diversity for European Russia and Transcaucasian countries were h = 0.56 ± 0.054; nucleotide diversity was π = 0.0016 ± 0.002. When we elongated the fragment of mtDNA (820 bp), haplotype (0.85 ± 0.03) and nucleotide diversity (π = 0.002 ± 0.001) were increased and 14 haplotypes were found. The geographic distribution of haplotypes depends neither on region nor river system. The central haplotype was detected throughout European Russia and Transcaucasian countries, as well as minor haplotypes, observed in a fewer number of regions. Therefore, the genetic diversity of Eurasian otter from European Russia and Transcaucasian countries is higher than in the rest of Europe. In addition, the population structure replicates the European pattern with several regional features. [ABSTRACT FROM AUTHOR]

The southern Italian peninsula has been suggested to be an important European district for lampreys' genetic diversity. All lamprey species ever described throughout the Italian peninsula are protected within European legislation and listed in Annex II of the EU Habitats Directive (92/43/EEC) and Annex III of the Bern Convention (82/72/CEE) as species of conservation concern, and the Habitats Directive ensures the designation of "sites of community interest" (SICs) for threatened species. During a survey to collect preliminary data on lampreys' presence in the Cilento, Vallo di Daino, and Alburni National Park (PNCV) located in the Campania region, where 28 sites of community interest (SICs) have been established by the EU Habitats Directive (92/43/EEC), two specimens of sea lamprey (Petromyzon marinus, Linnaeus, 1758) were detected for the first time. The specimens were genetically characterized through the sequencing of the mtDNA control region locus. The study highlighted the significant importance of the Campania region for lampreys, which, concerning Lampetra sp., was found to have peculiar genetic characteristics and unique alleles that have not been described elsewhere. Furthermore, the recognition of the sea lamprey, P. marinus, emphasized the value of this area, especially in terms of laying the groundwork for future habitat protection strategies. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) analysis has proven to be an excellent tool for studying the genetic ancestry of many populations. It is also helpful for forensic investigations because of its unique qualities, such as a high mutation rate, maternal mode of inheritance, a high quantity of copies in cells, and control region with specific genetic markers. Therefore, the present study is conducted to establish high-quality forensic data, as well as to assign predominant haplogroups by studying variations generated from mitochondrial DNA control regions among the south Indian Muslims. To this aim, 5ml blood samples were collected from 60 healthy unrelated Muslim individuals of Srirangapatna town in Karnataka state, South India. DNA extracted from the blood sample was amplified, and the sequence of the control region of mtDNA was determined by the Sanger method. Using these sequence data, 48 different haplotypes and 113 polymorphic positions were defined. Of the 48 haplotypes assessed, 40 were unique, and eight were observed in more than one individual. Diversity indices such as genetic diversity, power of discrimination, and random match probability were 0.9870, 0.9705, and 0.0294, respectively. The mean of pairwise differences was estimated at 14.671751 +/- 6.659951 and nucleotide diversity at 0.019229 +/- 0.009680. Consequently, the low random match probability and high genetic diversity were obtained from the present data, while previous studies suggest a high heterogeneity in the Indian Muslim population. The haplogroup pattern and its frequency were indicative of the composition of South Asian (52%), West Eurasian (28%), and West Asian (20%) genetic content in this population. The diversity indices and phylogenetic findings confirm the high potential of mtDNA control region polymorphisms in forensic investigation casework and phylogenetic studies. [ABSTRACT FROM AUTHOR]

To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus Amiota and six representative species in the genus Phortica. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the Amiota and Phortica mitogenomes ranged from 16,143–16,803 bp and 15,933–16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within Amiota and Phortica. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus Phortica. [ABSTRACT FROM AUTHOR]

Background. Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods. This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin. Results. Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon. Discussion. Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin. [ABSTRACT FROM AUTHOR]

The Amazonian snook (Centropomus irae) is the most recently described fish species of the genus Centropomus, which is endemic to the marine biogeographic region known as the Amazon River Plume, on the northern coast of Brazil. In the present study, we evaluated the population genetics, phylogeography, and evolutionary history of this species based on sequences of the Control Region of the mitochondrial genome. We analyzed a total of 87 specimens, including 39 C. irae and 48 specimens of the sister species Centropomus undecimalis, from the coast of the western South Atlantic. The results of the study revealed high levels of genetic diversity in both species, with no evidence of any genetic differentiation among the localities sampled for either species. This may be related to the typical migratory and reproductive behavior of the snooks. The analyses of the demographic history of the species identified a discrete process of population expansion in C. undecimalis at around 20,000 years ago, whereas C. irae passed through a marked population expansion approximately 30,000 years ago, which was probably linked to the formation of the Amazon plume and the fluctuations in sea levels that occurred during the late Pleistocene. [ABSTRACT FROM AUTHOR]

Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years. [ABSTRACT FROM AUTHOR]

The distribution and spread of the tundra vole (Alexandromys oeconomus) in Lithuania have been documented over the last 70 years, but the genetic diversity of the species has not been studied. In this study, we examined A. oeconomus trapped in three sites in northern and western Lithuania using mtDNA sequence analysis of the cytb and control region. The western and northern sites are separated by anthropogenic landscape barriers. The western site is subject to regular spring flooding. Phylogenetic analyses of the studied individuals placed them in the Central European phylogroup, suggesting that Lithuanian A. oeconomus originated from northeastern Poland. In Lithuania, the genetic diversity of A. oeconomus at both mtDNA loci was relatively low (Hd < 0.6, π < 0.002) compared to that found in other European samples (Hd = 0.833–0.958; π = 0.00402–0.01552). Individuals analyzed in Lithuania were genetically different from samples collected in Poland and Northern Europe (ΦST > 0.15, p < 0.05). The genetic divergence between the western and northern samples of A. oeconomus in Lithuania, together with the low genetic variability among the voles studied, provides new insights into the phylogeography of the species and the influence of barriers on the colonization of the country.

Background Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin. Results Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon. Discussion Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.

Simple Summary: The Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically important aquatic reptile species with rich nutrition and medicinal value. However, the wild resources of P. sinensis have been depleting due to natural and artificial factors in recent decades. Herein, we report the complete mitochondrial genomes of four P. sinensis strains and analyzed the nucleotide composition and variable site for the four mitogenomes. Using Ka/Ks and sliding window analyses, we explored the genetic diversity and selection pressures of different mitochondrial genes in the four P. sinensis strains. Through comparative analysis, the present study described the structural variation of 22 tRNAs, replication origin region of the L-strand, and control region, indicating the genetic variations among the four P. sinensis strains. Furthermore, the evolutionary relationship of P. sinensis strains and other Trionychidae species was determined by phylogenetic analysis. Taken together, our findings provide genetic information and an essential basis for understanding the genetic variations and evolutionary relationship of P. sinensis strains, which will play an important role in bioprospecting and conservation of P. sinensis. The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important aquaculture reptile with rich nutritional and medicinal values. In recent decades, the wild resources of P. sinensis have been depleting due to natural and artificial factors. Herein, we report the complete mitochondrial genome of four P. sinensis strains, including the Japanese (RB) strain, Qingxi Huabie (HB) strain, Jiangxi (JB) strain, and Qingxi Wubie (WB) strain. The nucleotide composition within the complete mitogenomes was biased towards A + T with a variable frequency ranging from 59.28% (cox3) to 70.31% (atp8). The mitogenomes of all four strains contained 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, 1 control region, and a replication origin region of the L-strand replication (OL), which was consistent with most vertebrates. Additionally, the atp8, nad4l, nad6, and nad3 genes possessed high genetic variation and can be used as potential markers for the identification of these P. sinensis strains. Additionally, all PCGs genes were evolving primarily under purifying selection. Through comparative analysis, it was revealed that most of the tRNAs were structurally different in the TψC stem, DHU stem, and acceptor stem. The length of the tandem repeats in the control region was variable in the four P. sinensis strains, ranging from 2 bp to 50 bp. Phylogenetic analysis indicated that all P. sinensis strains clustered into one branch and were closely related to other Trionychinae species. Overall, this study provides mitochondrial genome information for different P. sinensis strains to support further species identification and germplasm resource conservation. [ABSTRACT FROM AUTHOR]

Daphnia galeata is an important plankton in aquatic ecosystems. As a widely distributed species, D. galeata has been found throughout the Holarctic region. Understanding the genetic diversity and evolution of D. galeata requires the accumulation of genetic information from different locations. Even though the mitochondrial genome (mitogenome) sequence of D. galeata has already been reported, little is known about the evolution of its mitochondrial control region. In this study, D. galeata samples were collected from the Han River on the Korean Peninsula and its partial nd2 gene was sequenced for haplotype network analysis. This analysis showed that four clades of D. galeata were present in the Holarctic region. Moreover, the D. galeata examined in this study belonged to clade D and was specific to South Korea. The mitogenome of D. galeata from the Han River showed similar gene content and structure compared to sequences reported from Japan. Furthermore, the structure of control region of the Han River was similar to those of Japanese clones and differed substantially from European clone. Finally, a phylogenetic analysis based on the amino acid sequences of 13 protein-coding genes (PCGs) indicated that D. galeata from the Han River formed a cluster with clones collected from Lakes Kasumigaura, Shirakaba, and Kizaki in Japan. The differences in control region structure and stem and loop structure reflect the different evolutionary directions of the mitogenomes from Asian and European clones. These findings improve our understanding of the mitogenome structure and genetic diversity of D. galeata. [ABSTRACT FROM AUTHOR]