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Maize is an important cereal crop with multipurpose applications. In this experiment normal and mutant plant leaves were analyzed for understanding the mechanism of mutation in cp DNA and mt DNA. From the leaf material, cp DNA and mt DNA were isolated and sequenced using standard techniques, and annotation was done with bioinformatics tools and software. The data revealed marked variations in these organelle genomes. In cp DNA, marked variations in three genes i.e. (i) rpl36, (ii) ndhF and (iii) ccsA were evident by base pair addition/deletion and SNPs at various positions. Similarly, in mt DNA also five genes showed noticeable variations in mat-r, ccmfN, rps12, rps2B, and rps2A in base pair additions and SNPs. These mutations may play an important role in the development of mutant maize plants. [ABSTRACT FROM AUTHOR]

Spalerosophis Jan, 1865, is a colubrid snake genus distributed in arid and semiarid regions from northwestern Africa to northern India. Six species of Spalerosophis are identified based on traditional morphology; however, there are arguments about their systematic status. We performed the first molecular phylogenetic analyses for this genus using nucleotide sequences of c. 2278 bp from three mitochondrial genes (12S rRNA, 16S rRNA, and cyt b) to investigate the phylogenetic relationships and historical evolution of the poorly known Spalerosophis species and doubtful populations. We used fossil calibrations for dating divergences. Our phylogenetic analyses clearly showed five separate species with high support values, including S. arenarius, S. atriceps, S. microlepis, S. diadema schirasianus, and S. diadema cliffordii. Bayesian calibrated molecular clock suggested that the genus Spalerosophis diverged from the common ancestor in the Paleogene around 35.28 Mya (25.89–44.66). Our analysis indicated that isolated S. atriceps was separated around 21.72 Mya (10.86–33.04) as the basal diverged species of the genus. This suggested that the species of Spalerosophis probably originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Spalerosophis arenarius and S. atriceps were identified as the two last diverged members of the genus, separated from S. d. schirasianus during the Middle Miocene about 13.31 Mya (5.52–22.33). These results indicate that the separation of Spalerosophis species coincided with the orogenic events of the Zagros Mountains in western Iran and the Sulaiman Mountains in Afghanistan, India, and Pakistan. Their diversification may therefore be the result of vicariance events that promoted their current distribution. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of the genus Spalerosophis and highlights the need for more molecular studies on unknown snakes. [ABSTRACT FROM AUTHOR]

The family Gobiidae is the largest teleost family, consisting of more than 2,000 species in more than 200 genera. They have adapted to a wide range of habitats, inhabiting mostly marine and brackish waters. Recently invasive Ponto-Caspian gobies have caused significant changes to the structure of fish assemblage throughout the European waters. The aim of the study was to verify the possibility of identifying three species of the genus Gobiidae based on the analysis of the mitochondrial region of the cytochrome oxidase subunit 1 (COI) gene. 339 samples originated from seven countries and 17 different sites were investigated. Qualitative and quantitative assessment of the extracted DNA was conducted by measuring light absorbance and electrophoretic separation. Approximately 650-bp (base pairs) fragments were amplified from the 5' region of the mitochondrial COI with the PCR (polymerase chain reaction) reaction. Sequences of 652 bp were obtained and compared with reference sequences in the National Center for Biotechnology Information (NCBI). Based on the sequence analysis, we determined that in the analysed geographical regions, the goby preliminary identified morphologically as the round goby was represented by three species: round goby (Neogobius melanostomus), tubenose goby (Proterorhinus marmoratus), and monkey goby (Neogobius fluviatilis). The latter two are newly reported for their new habitats. Genetic characterisation of such populations offers the opportunity to assess their genetic stability, which provides agencies managing the aquatic environment in EU countries with a tool for revising the legislation, including regulations relevant for updating the status of native and invasive species in European waters. [ABSTRACT FROM AUTHOR]

Graphoderus bilineatus is a predacious diving beetle, widely distributed across Europe. Its poor dispersal ability and the fragmentation and deterioration of its habitats have been indicated as the major causes of decline. In several western European countries, the species is extinct, justifying its inclusion as “vulnerable” in the IUCN red list. Aiming for the conservation of the last known population of G. bilineatus in the northern Italian region of Emilia Romagna, at the lake Pratignano, we surveyed its genetic diversity at the mitochondrial COI gene and compared it to that of other European populations. Two fixed COI haplotypes were found in the Italian and Austrian populations, respectively. Both haplotypes were unique among the European populations surveyed, suggesting these populations suffered a bottleneck and geographic isolation. Populations in western Europe showed lower genetic diversity and higher degree of differentiation than eastern populations. The uniqueness of Pratignano haplotype makes it difficult to choose a source population from which to transfer animals for a possible restocking. Selection of the source population should be based mainly on ecological considerations, but at the same time ensuring a good genetic diversity to maximize the adaptive potential.

Background: In the third era of ancient DNA field, it has endured the mesmerising modifications, which should be revealed. From side to side period, analysis of mitochondrial DNA permits to determine the evolutionary relationship among the species, to expose the terrestrial roots of the entities, to standardise the molecular clocks and to study the demographic pasts. Methods: In the current study we used bioinformatics tools for prediction of mitochondrial haplogroups and phylogenetic analysis. The ancient complete mitochondrial genomes were retrieved from online resources and were further used for phylogenetic analysis to know the evolutionary position of the ancient populations lived thousands of years ago. Results: We aligned 46 ancient genomes, collected online and estimated trees by using neighbour-joining, maximum parsimony and maximum-likelihood. Support for nodes was assessed with bootstrap replicates. During our analysis a strong bond between genomes of Altai Neanderthal, Motala 12, Motala 1, Loschbour, Ust'-Ishim, LBK, Mezmaiskaya Neanderthal, Denisova, RISE391(ERR844272), Clovis Anzick-1, RISE395(ERR844275) and RISE210(ERR844262) were found. In this context these ancient samples recommended the presence of a mutual earliest genomic signature. Conclusion: A significant population immigrations and alternates, accountable for influencing main parts of current demographic structure together in Europe and Asia is supported by the Bot15 (ERR668415) and RISE family. In the initial bronze period, ancestral similarity among these populations also share the theorised blow-out of Indo-European languages. Mechanisms of pathogen development and alteration for evolving and reappearing toxicities is also explained by this study. We aim that this study will help researchers in understanding the evolutionary position of ancient populations resided around the world.

The sculpins Cottus metae and C. scaturigo have previously been distinguished morphologically from C. gobio and described as distinct species. In the present study, sculpin samples from numerous sites covering the proposed range of C. metae and C. scaturigo, including unexamined adjacent sites that include topotypic specimens and other sculpins, were examined to determine whether they represent phylogenetically distinct units and to determine the geographical limits of the distribution of C. metae. Using two types of marker—the mitochondrial control region and the nuclear large subunit of the ribosomal RNA gene—we found high statistical support for C. gobio and C. metae forming two distinct clades. A sister relationship between C. gobio and C. metae was observed but also indicating, by analogy to the well‐established status of the former, that the latter is a distinct species. However, this conclusion does not apply to C. scaturigo as the sample from the type locality clustered with C. gobio. A survey of numerous sculpin localities in Slovenia and adjacent areas, including the Drava river system, found that C. metae populates only the Sava river system, from the headwaters in NW Slovenia to the Medveščak Stream at Zagreb, Croatia. However, further downstream in the Kolpa River, and also in the Lonja and Una river systems, the next two tributaries to the Sava River, a sculpin population genetically distinct from both C. metae and C. gobio was found. [ABSTRACT FROM AUTHOR]

Thalamita danae (Stimpson1858), re-described as a new report, based on an integrative taxonomy approach combining 16S rRNA partial sequence of mitochondrial DNA and morphological analyses was used for the accurate identification of specimens. The morphological and molecular analysis provides the confirm evidence of T. danae in coastal waters of Pakistan. Results were confirmed by amplification of partial sequences of 16S rRNA mt-DNA gene and the sequence was searched for similarity using BLASTn (Basic Local Alignment Tool), the result showed 97% sequence similarity with partial sequences of T. danae Stimpson, 1858 as obtained from gene bank. The attained sequence was submitted to gene bank after confirmation of genetic and morphological similarity. High sequence similarity with accession no: FJ152165.1 indicated, that misidentification of species does not occur.

Graphoderus bilineatus is a predacious diving beetle, widely distributed across Europe. Its poor dispersal ability and the fragmentation and deterioration of its habitats have been indicated as the major causes of decline. In several western European countries, the species is extinct, justifying its inclusion as "vulnerable" in the IUCN red list. Aiming for the conservation of the last known population of G. bilineatus in the northern Italian region of Emilia Romagna, at the lake Pratignano, we surveyed its genetic diversity at the mitochondrial COI gene and compared it to that of other European populations. Two fixed COI haplotypes were found in the Italian and Austrian populations, respectively. Both haplotypes were unique among the European populations surveyed, suggesting these populations suffered a bottleneck and geographic isolation. Populations in western Europe showed lower genetic diversity and higher degree of differentiation than eastern populations. The uniqueness of Pratignano haplotype makes it difficult to choose a source population from which to transfer animals for a possible restocking. Selection of the source population should be based mainly on ecological considerations, but at the same time ensuring a good genetic diversity to maximize the adaptive potential. [ABSTRACT FROM AUTHOR]

Thalamita danae (Stimpson1858), re-described as a new report, based on an integrative taxonomy approach combining 16S rRNA partial sequence of mitochondrial DNA and morphological analyses was used for the accurate identification of specimens. The morphological and molecular analysis provides the confirm evidence of T. danae in coastal waters of Pakistan. Results were confirmed by amplification of partial sequences of 16S rRNA mt-DNA gene and the sequence was searched for similarity using BLASTn (Basic Local Alignment Tool), the result showed 97% sequence similarity with partial sequences of T. danae Stimpson, 1858 as obtained from gene bank. The attained sequence was submitted to gene bank after confirmation of genetic and morphological similarity. High sequence similarity with accession no: FJ152165.1 indicated, that misidentification of species does not occur. [ABSTRACT FROM AUTHOR]

Diabetic retinopathy is a neurovascular diabetes complication resulting in vision loss. A wealth of literature reports retinal molecular changes indicative of neural deficits, inflammation, and vascular leakage with chronic diabetes, but the mechanistic causes of disease initiation and progression are unknown. Microvascular mitochondrial DNA (mt DNA) damage leading to mitochondrial dysfunction has been proposed to drive vascular dysfunction in retinopathy. However, growing evidence suggests that neural retina dysfunction precedes and may cause vascular damage. Therefore, we tested the hypothesis that neural mt DNA damage and mitochondrial dysfunction are an early initiating factor of neural diabetic retinopathy development in a rat streptozotocin-induced, Type I diabetes model. Mitochondrial function (oxygen consumption rates) was quantified in retinal synaptic terminals from diabetic and non-diabetic rats with paired retinal structural and function assessment (optical coherence tomography and electroretinography, respectively). Mitochondrial genome damage was assessed by identifying mutations and deletions across the mt DNA genome by high depth sequencing and absolute mt DNA copy number counting through digital PCR. Mitochondrial protein expression was assessed by targeted mass spectrometry. Retinal functional deficits and neural anatomical changes were present after 3 months of diabetes and prevented/normalized by insulin treatment. No marked dysfunction of mitochondrial activity, maladaptive changes in mitochondrial protein expression, alterations in mt DNA copy number, or increase in mt DNA damage was observed in conjunction with retinal functional and anatomical changes. These results demonstrate that neural retinal dysfunction with diabetes begins prior to mt DNA damage and dysfunction, and therefore retinal neurodegeneration initiation with diabetes occurs through other, non-mitochondrial DNA damage, mechanisms. [ABSTRACT FROM AUTHOR]

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population. [ABSTRACT FROM AUTHOR]

Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean ( SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal-offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal ( n = 127) and offshore ( n = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mt DNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites FST = 0.385, p < .001; mt DNA FST = 0.183, p < .001; Φ ST = 0.385, p < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential 'contact zones', we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit ( ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed. [ABSTRACT FROM AUTHOR]

Aim We examine the influence of fluctuating sea levels in a land-bridge archipelago on the apportioning of intraspecific genetic diversity and divergence in the widespread Puerto Rican crested anole ( Anolis cristatellus). We compare three alternative scenarios for genetic diversification in an archipelagic species that contrast the relative influences of periodic isolation versus island connectedness driven by fluctuating sea levels. Our approach combines information from geography and population genetics to assess the influence of island size, island isolation, island historical geography, and population genetic processes such as drift on the contemporary distribution of genetic variation within and among islands. Location The Puerto Rico Bank in the Caribbean focusing primarily on the Spanish, British and U.S. Virgin Islands. Methods We used nuclear and mitochondrial DNA sequences and microsatellite genotypes sampled from A. cristatellus populations to investigate: (1) the broad-scale pattern of phylogeographical divergence across Puerto Rico Bank islands and (2) diversification within the Virgin Islands archipelago. For the first component, we used sequence data to reconstruct the relationships among 542 samples from across the species range. For the second component, we examined the relative influences of island size, isolation, and population genetic processes on the distribution of genetic diversity across the Virgin Islands. Results In the Virgin Islands, A. cristatellus is represented by a monophyletic clade except on the island of Vieques, where two divergent clades coexist. We found evidence for non-equilibrium dynamics in the Virgin Islands, suggesting spatial population expansion during intraglacial periods of low sea level. Main conclusions We found limited evidence that periods of island isolation affected patterns of genetic diversity and differentiation. Instead, we found that the patterns of genetic diversity and divergence in A. cristatellus in the Virgin Islands archipelago are likely shaped by long-term persistence in the region and periods of population spatial expansion. [ABSTRACT FROM AUTHOR]

Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms. [ABSTRACT FROM AUTHOR]

Genetic differentiation among Spotted Owl ( Strix occidentalis) subspecies has been established in prior studies. These investigations also provided evidence for introgression and hybridization among taxa but were limited by a lack of samples from geographic regions where subspecies came into close contact. We analyzed new sets of samples from Northern Spotted Owls ( NSO: S. o. caurina) and California Spotted Owls ( CSO: S. o. occidentalis) in northern California using mitochondrial DNA sequences (mt DNA) and 10 nuclear microsatellite loci to obtain a clearer depiction of genetic differentiation and hybridization in the region. Our analyses revealed that a NSO population close to the northern edge of the CSO range in northern California (the NSO Contact Zone population) is highly differentiated relative to other NSO populations throughout the remainder of their range. Phylogenetic analyses identified a unique lineage of mt DNA in the NSO Contact Zone, and Bayesian clustering analyses of the microsatellite data identified the Contact Zone as a third distinct population that is differentiated from CSO and NSO found in the remainder of the subspecies' range. Hybridization between NSO and CSO was readily detected in the NSO Contact Zone, with over 50% of individuals showing evidence of hybrid ancestry. Hybridization was also identified among 14% of CSO samples, which were dispersed across the subspecies' range in the Sierra Nevada Mountains. The asymmetry of hybridization suggested that the hybrid zone may be dynamic and moving. Although evidence of hybridization existed, we identified no F1 generation hybrid individuals. We instead found evidence for F2 or backcrossed individuals among our samples. The absence of F1 hybrids may indicate that (1) our 10 microsatellites were unable to distinguish hybrid types, (2) primary interactions between subspecies are occurring elsewhere on the landscape, or (3) dispersal between the subspecies' ranges is reduced relative to historical levels, potentially as a consequence of recent regional fires. [ABSTRACT FROM AUTHOR]

The taxonomic status of Rhinolophus macrotis sensu lato (s.l.) in Vietnam and adjacent territories remains problematic. To address this issue, we performed an integrated study of morphological, acoustic, and genetic characters of R. macrotis s.l. specimens and compared these with sympatric species within the philippinensis group ( R. marshalli, R. paradoxolophus, and R. rex). Our results reveal that in addition to a cryptic species of R. macrotis previously found in Jiangxi and Jingmen, China, R. macrotis s.l. in continental Asia includes three further species, namely R. cf . siamensis, R. cf . macrotis, and R. cf . macrotis 'Phia Oac.' These four taxa are distinguished from genuine R. macrotis in Nepal and R. siamensis in Thailand by their morphological and/or genetic features. Further taxonomic evaluation of the subspecies of R. macrotis s.l. is needed to determine their affinities with recently recognized cryptic species and to possibly describe new taxa. Our results also show that interspecific divergences in mitochondrial DNA sequences ( Cytb and COI genes) among taxa within the philippinensis group (particularly between R. cf. siamensis/ R. cf . macrotis and R. rex/ R. paradoxolophus) are significantly lower than those of other morphological groups in the genus. These phylogenetic patterns might be explained by recent allopatric speciation or ancient introgression events among ancestors of the taxa during the Pleistocene. However, further investigations including genetic analyses of nuclear genes are needed to test the latter hypothesis. [ABSTRACT FROM AUTHOR]

Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens. [ABSTRACT FROM AUTHOR]

We examine the use of an ensemble method, Random Forests, to delimit subspecies using mitochondrial DNA (mt DNA) sequences. Diagnosability, a measure of the ability to correctly determine the taxon of a specimen of unknown origin, has historically been used to delimit subspecies, but few studies have explored how to estimate it from DNA sequences. Using simulated and empirical data sets, we demonstrate that Random Forests produces classification models that perform well for diagnosing subspecies and species. Populations with strong social structure and relatively low abundances ( e.g., killer whales, Orcinus orca) were found to be as diagnosable as species. Conversely, comparisons involving subspecies that are abundant ( e.g., spinner and spotted dolphins, Stenella longirostris and S. attenuata), are only as diagnosable as many population comparisons. Estimates of diagnosability reported in subspecies and species descriptions should include confidence intervals, which are influenced by the sample sizes of the training data. We also stress the importance of reporting the certainty with which individuals in the training data are classified in order to communicate the strength of the classification model and diagnosability estimate. Guidance as to ideal minimum diagnosability thresholds for subspecies will improve with more comprehensive analyses; however, values in the range of 80%-90% are considered appropriate. [ABSTRACT FROM AUTHOR]

The Purple Sandpiper ( Calidris maritima) is a medium-sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Migration routes and affiliations between breeding grounds and wintering grounds are incompletely understood. Some populations appear to be declining, and future management policies for this species will benefit from understanding their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and historical demographic trends. Samples were obtained from breeding locations in Nunavut (Canada), Iceland, and Svalbard (Norway) and from wintering locations along the coast of Maine (USA), Nova Scotia, New Brunswick, and Newfoundland (Canada), and Scotland (UK). Mitochondrial haplotypes displayed low genetic diversity, and a shallow phylogeny indicating recent divergence. With the exception of the two Canadian breeding populations from Nunavut, there was significant genetic differentiation among samples from all breeding locations; however, none of the breeding populations was a monophyletic group. We also found differentiation between both Iceland and Svalbard breeding populations and North American wintering populations. This pattern of divergence is consistent with a previously proposed migratory pathway between Canadian breeding locations and wintering grounds in the United Kingdom, but argues against migration between breeding grounds in Iceland and Svalbard and wintering grounds in North America. Breeding birds from Svalbard also showed a genetic signature intermediate between Canadian breeders and Icelandic breeders. Our results extend current knowledge of Purple Sandpiper population genetic structure and present new information regarding migration routes to wintering grounds in North America. [ABSTRACT FROM AUTHOR]

Marine mussels of the family Mytilidae, as well as a number of other bivalves, have a unique system of mitochondrial DNA inheritance called doubly uniparental inheritance ( DUI). DUI is characterized by the presence of an 'F' mitochondrial genome that is transmitted through mothers to daughters and sons, and an 'M' mitochondrial genome that is transmitted only from fathers to sons. In this paper, we demonstrate that DUI exists in the horse mussel, Modiolus modiolus (Linnaeus, 1758) and compare the pattern of molecular evolution of the M and F types in this species. Total DNA was isolated from M. modiolus male and female gonad tissues, as well as from spawned sperm cells. From these DNA samples, partial mitochondrial DNA fragments were amplified from both cytochrome c oxidase subunit I ( cox1), and 16S ribosomal RNA ( rrnL) genes. Based on cox1 and rrnL sequences, heteroplasmy was observed in M. modiolus and characterized by the resolution of two mitotypes: an F mitotype present in tissues of both males and females, and an M mitotype present in spawned sperm. Using standardized p-distance and Tamura-Nei values, M. modiolus is found to display the highest M/F conspecific sequence divergence for any member of the family Mytilidae (i.e. 38% M/F sequence divergence, which is 9% higher than any other intraspecific M/F comparison for the family Mytilidae when standardized using p-distances across all taxa observed). Sequence analysis also indicated that the M. modiolus M mitotype evolves significantly faster than its conspecific F type. The findings discussed herein broaden the range of mytilid species known to exhibit DUI and they also establish a new threshold for the genetic divergence of male mytilid mitochondrial genomes. [ABSTRACT FROM AUTHOR]

Freshwater truncatelloidean gastropods include numerous minute cryptic species, displaying simple morphologies, all of which hampers their taxonomic research based on morphology. Phylogenetic relationships among all but one extant species of the genus Kerkia from five localities in Croatia and one in Slovenia were therefore analysed based on one mitochondrial ( cytochrome c oxidase subunit I) and three nuclear markers ( 18S, 28S and H3). Kerkia kusceri (Bole, ), K. jadertina Kuščer, 1933, K. j. sinjana (Kuščer, 1933), and K. kareli Beran, Bodon et Cianfanelli, 2014, were collected from their type localities. Our analysis confirmed their distinctness, recovering two additional clades that may represent yet undescribed species from Croatia. Apart from Kerkia, Hauffenia media Bole, , H. subpiscinalis (Kuščer, 1932) and H. erythropomatia (Hauffen, 1856) from Slovenia were analysed. Their distinctness together with the rejection of the eligibility for separate genus Erythropomatiana for the latter species was proven. Interestingly, its sequence divergence exceeded all previous estimates for species-level divergence within the Truncatelloidea, implying a species-level separation both for the COI and for nuclear loci. High p-distances for the COI/nuclear loci (0.128/0.027, respectively) confirmed also the uniqueness of both genera. A comparison of their COI sequences with the reference sequences of Alzoniella Giusti et Bodon, 1984, Avenionia Nicolas, 1882, Fissuria Boeters, 1981, and Agrafia Szarowska et Falniowski, 2011, has shown that Kerkia and Hauffenia are not sister clades. The most striking, however, was the apparent introgression of the ' Hauffenia' mt DNA type from central Slovenia (cave Babja luknja) into two Kerkia clades from central (Ljubač) and southern (Podgrađe) Croatia, that are located 210 km and 360 km away, respectively. The introduced ' Hauffenia' mt DNA type and the closest Hauffenia erythropomatia COI differed by 0.8%. Secondary loss of isolating mechanisms between phylogenetically distant organisms and the severe lack of information on distribution of these underground taxa were postulated as possible explanations of this interesting phenomenon. [ABSTRACT FROM AUTHOR]

Horizontal gene transfer ( HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mt DNA) have been largely unexplored., We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT., The sequencing of the complete mt DNA of L. mirabile revealed the unprecedented acquisition of host-derived mitochondrial genes, representing 80% of the protein-coding gene content. All but two of these foreign genes replaced the native homologs and are probably functional in energy metabolism. The genome consists of 54 circular-mapping chromosomes, 25 of which carry no intact genes., The likely functional replacement of up to 26 genes in L. mirabile represents a stunning example of the potential effect of rampant HGT on plant mitochondria. The use of host-derived genes may have a positive effect on the host-parasite relationship, but could also be the result of nonadaptive forces. [ABSTRACT FROM AUTHOR]

Humpback whales wintering in tropical waters along the Atlantic and Pacific coasts of the South American continent are thought to represent distinct populations or 'stocks.' Here we present the first analysis of genetic differentiation and estimates of gene flow between these breeding stocks, based on both mitochondrial DNA (mt DNA) control region sequences (465 bp) and 16 microsatellite loci from samples collected off Brazil ( n = 277) and Colombia ( n = 148), as well as feeding areas near the western Antarctic Peninsula ( n = 86). We found significant differentiation between Brazilian and Colombian breeding grounds at both mt DNA ( F ST = 0.058) and microsatellite ( F ST = 0.011) markers and corroborated previous studies showing genetic similarity between humpbacks from Colombia and those from Antarctic Peninsula feeding areas. Estimates of long-term gene flow between Brazil and Colombia were low to moderate, asymmetrical, and mostly mediated by males. Assignment procedures detected some cases of interchange and individuals of admixed ancestry between breeding grounds, indicating limited mixing of individuals between these stocks. Overall, results highlight the differentiation of humpback whale breeding populations with adjacent feeding grounds. This appears to be a remarkable example of fidelity to seasonal habitat in the absence of any contemporary barriers. [ABSTRACT FROM AUTHOR]

Aim Predicting species responses to global change is one of the most pressing issues in conservation biogeography. A key part of the problem is understanding how organisms have reacted to climatic changes in the past. Here, we use species distribution modelling to infer the effects of climate changes since the Last Interglacial ( LIG, c. 130,000 yr bp) on patterns of genetic structure and diversity in the western spadefoot toad ( Pelobates cultripes) in combination with spatially explicit phylogeographical analyses. Location Iberian Peninsula and mainland France. Methods Five hundred and twenty-four individuals from 54 populations across the species range were sampled to document patterns of genetic diversity and infer their evolutionary history based on data from mt DNA and 14 polymorphic microsatellites. Generalized linear models based on distribution data were used to infer climatic favourability for the species in the present and in palaeoclimatic simulations for the LIG, the mid-Holocene and the Last Glacial Maximum (LGM). Results Estimates of genetic diversity show a decreasing trend from south to north, suggesting persistence of high historical population sizes in the southern Iberian Peninsula. Species distribution models show differences in climatic favourability through time, with significant correlations between historically stable favourable areas and current patterns of genetic diversity. These results are corroborated by Bayesian skyline plots and continuous diffusion phylogeographical analyses. Main conclusions The results indicate the presence of southern refugia, with moderate recent expansions at the northern end of the species' range. Toads at the northern range margin exhibit the lowest genetic diversity and occupy areas of high past climate variability, classified as marginal in terms of favourability, rendering these populations most vulnerable to climate-mediated changes in the long term. [ABSTRACT FROM AUTHOR]

To understand the maternal genetic diversity of Tianzhu white yak better, we analyzed mt DNA D-loop sequences of 209 Tianzhu white yaks, which are from the central region of Tianzhu white yak habitat. Accordingly, a total of 45 haplotypes were identified in Tianzhu white yaks in this study, and 18 of them were unique. The nucleotide diversity and haplotype diversity of population studied were 0.024 ± 0.003 and 0.946 ± 0.007 respectively, revealing that Tianzhu white yak possess a relatively high genetic diversity. The phylogenetic analysis, combining D-loop sequences in this study with 533 previous published D-loop sequences of 13 yak breeds, indicated that Tianzhu white yaks fell mainly into haplogroup A and that a small portion belonged to haplogroups B, C, D and E. Moreover, six haplotypes of 20 individuals identified in Tianzhu white yak were in the taurine haplogroup, indicating hybridization between Bos taurus and Tianzhu white yaks. In summary, this study supplies a comprehensive maternal genetic pattern for Tianzhu white yak and provides a basic reference for future breeding programs to conserve the purebred Tianzhu white yak. [ABSTRACT FROM AUTHOR]

For elusive mammals like bats, colonization of new areas and colony formation are poorly understood, as is their relationship with the genetic structure of populations. Understanding dispersal and group formation behaviors is critical not only for a better comprehension of mammalian social dynamics, but also for guiding conservation efforts of rare and endangered species. Using nuclear and mitochondrial markers, we studied patterns of genetic diversity and differentiation among and within breeding colonies of giant noctule bats ( Nyctalus lasiopterus), their relation to a new colony still in formation, and the impact of this ongoing process on the regionwide genetic makeup. Nuclear differentiation among colonies was relatively low and mostly nonsignificant. Mitochondrial variation followed this pattern, contrasting with findings for other temperate bat species. Our results suggest that this may indicate a recent population expansion. On average, female giant noctules were not more closely related to other colony members than to foreign individuals. This was also true for members of the newly forming colony and those of another, older group sampled shortly after its formation, suggesting that contrary to findings for other temperate bats, giant noctule colonies are not founded by relatives. However, mother-daughter pairs were found in the same populations more often than expected under random dispersal. Given this indication of philopatry, the lack of mitochondrial differentiation among most colonies in the region is probably due to the combination of a recent population expansion and group formation events. [ABSTRACT FROM AUTHOR]

Aim Identification of potential glacial refugia and post-glacial colonization processes of a flightless, cold-adapted ground beetle Location Central and eastern Europe. Methods We analysed the genetic structure of 33 Carabus sylvestris populations sampled across its entire distribution range using nuclear and mitochondrial markers. We further compiled occurrence records to develop species distribution models to predict distribution ranges for the last glacial period and the present based on the species' current climatic niche. Results Distinct genetic lineages were detected for a number of mountain ranges and were congruent for both molecular marker systems. Most genetic splits were the results of vicariance, whereas dispersal was rare. Our models suggest that the species' distribution range was larger and more interconnected in the past. Main conclusions Our data support multiple glacial refugia for C. sylvestris, some of which were located north of the Alps. Some lower mountain ranges were likely recolonized post-glacially. [ABSTRACT FROM AUTHOR]

The loggerhead turtle, Caretta caretta, is a highly migratory species with a complex life cycle that involves a series of ontogenetic habitat shifts and migrations. Understanding the links amongst nesting populations and foraging habitats is essential for the effective management of the species. Here we used mixed stock analysis to examine the natal origin of loggerhead turtles foraging on the North African continental shelf off Tunisia, one of the most important Mediterranean neritic habitats. An 815-bp fragment of the mitochondrial DNA control region was sequenced from 107 individuals sampled from 2007 to 2009. No temporal variation in haplotype frequencies was detected. Juveniles (n = 87) and adults (n = 23) exhibited weak but significant genetic differentiation that resulted in different stock compositions. Libya was the main source population but the proportion of turtles from this rookery was higher in adults (median = 80%) than in juveniles (median = 35%). Western Greece was the second most important contributing population. Juvenile stock composition derived from mixed stock analysis and the estimates produced by numerical simulation of hatchling dispersion in the Mediterranean Sea were significantly correlated, supporting the recent theory that loggerheads imprint on possible future neritic habitats during the initial phase of their life. This association was not significant for adults, suggesting that other factors contribute to shaping their distribution. Overall, our results show that human activities on the South Tunisian continental shelf pose an immediate threat to the survival of the Libyan rookery. [ABSTRACT FROM AUTHOR]

Continuous animal populations often become fragmented due to anthropogenic habitat alterations. These small, fragmented populations are fragile due to demographic and genetic factors, whereas immigration can enhance their long-term viability. Previously, we showed that high philopatry affected the local dynamics of three small and remnant subpopulations of Northern Wheatears in The Netherlands. Here, we show that these three populations together with an additional larger population in the European lowlands are highly genetically differentiated based on 22 microsatellite markers. In contrast, we found no evidence for differentiation using two mitochondrial DNA markers. An IMa2 analysis indicates that gene flow has occurred regularly among our sampled populations. As immigration of colour-ringed birds among our sampled populations is rare at best, our results suggest that the populations have recently become isolated from one another. Low dispersal rates in highly mobile birds may occur when suitable habitat becomes highly fragmented, and will accentuate stochastic demographic processes and inbreeding, both reducing population viability. As dispersal rates are low among populations of Northern Wheatears in The Netherlands, there is only a small probability of recolonization of habitat patches where populations have become locally extinct. [ABSTRACT FROM AUTHOR]

Steep genetic clines resulting from recent secondary contact between previously isolated taxa can either gradually erode over time or be stabilized by factors such as ecological selection or selection against hybrids. We used patterns of variation in 30 nuclear and two mitochondrial SNPs to examine the factors that could be involved in stabilizing clines across a hybrid zone between two subspecies of the Atlantic killifish, Fundulus heteroclitus. Increased heterozygote deficit and cytonuclear disequilibrium in populations near the center of the mt DNA cline suggest that some form of reproductive isolation such as assortative mating or selection against hybrids may be acting in this hybrid zone. However, only a small number of loci exhibited these signatures, suggesting locus-specific, rather than genomewide, factors. Fourteen of the 32 loci surveyed had cline widths inconsistent with neutral expectations, with two SNPs in the mitochondrial genome exhibiting the steepest clines. Seven of the 12 putatively non-neutral nuclear clines were for SNPs in genes related to oxidative metabolism. Among these putatively non-neutral nuclear clines, SNPs in two nuclear-encoded mitochondrial genes ( SLC25A3 and HDDC2), as well as SNPs in the myoglobin, 40S ribosomal protein S17, and actin-binding LIM protein genes, had clines that were coincident and concordant with the mitochondrial clines. When hybrid index was calculated using this subset of loci, the frequency distribution of hybrid indices for a population located at the mt DNA cline center was non-unimodal, suggesting selection against advanced-generation hybrids, possibly due to effects on processes involved in oxidative metabolism. [ABSTRACT FROM AUTHOR]

The European stag beetle Lucanus cervus, widely distributed across Europe and in some Near East countries, is one of the best known coleopteran species listed in the European Habitats Directive 92/43/ EEC and it is considered a flagship species for conservation of saproxylic fauna. Lucanus tetraodon is a closely related species whose geographical distribution is still poorly known and debated. The two species have a sympatric occurrence in central Italy, and in some localities of these areas, many individuals show a mosaic of morphological traits that makes species assignment nearly impossible. We used both mitochondrial and nuclear markers to analyse these specimens. The mitochondrial results evidenced that the two species represent well-defined genetic entities with mitochondrial DNA introgression. This pattern could be the result of either hybridization or of a convergence of morphological characters under local selective pressures in areas of sympatric occurrence. The nuclear marker was polymorphic across the two species and therefore did not reveal hybridization, even if many are the supports to this phenomenon. The most plausible explanation for this genetic pattern is a very recent divergence of the two species which share a common origin and thus a common wg genotype. [ABSTRACT FROM AUTHOR]

Generalist parasites exploit multiple host species at the population level, but the individual parasite's strategy may be either itself a generalist or a specialist pattern of host species use. Here, we studied the relationship between host availability and host use in the individual parasitism patterns of the Shiny Cowbird Molothrus bonariensis, a generalist avian obligate brood parasite that parasitizes an extreme range of hosts. Using five microsatellite markers and an 1120-bp fragment of the mt DNA control region, we reconstructed full-sibling groups from 359 cowbird eggs and chicks found in nests of the two most frequent hosts in our study area, the Chalk-browed Mockingbird Mimus saturninus and the House Wren Troglodytes aedon. We were able to infer the laying behavior of 17 different females a posteriori and found that they were mostly faithful to a particular laying area and host species along the entire reproductive season and did not avoid using previously parasitized nests (multiple parasitism) even when other nests were available for parasitism. Moreover, we found females using the same host nest more than once (repeated parasitism), which had not been previously reported for this species. We also found few females parasitizing more than one host species. The use of an alternative host was not related to the main hosts' nest availability. Overall, female shiny cowbirds use a spatially structured and host species specific approach for parasitism, but they do so nonexclusively, resulting in both detectable levels of multiple parasitism and generalism at the level of individual parasites. [ABSTRACT FROM AUTHOR]

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mt DNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mt DNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394-bp mt DNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mt DNA diversity (π = 0.430%) reflecting an expansion event <80 000 years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to male-mediated gene flow. A hierarchical amova showed that regions were important for explaining mt DNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mt DNA and microsatellite variance within both oceans. Therefore, both geographic philopatry and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behaviour, geographic features and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization. [ABSTRACT FROM AUTHOR]

Glacial phases during the Pleistocene caused remarkable changes in species range distributions, with inevitable genetic consequences. Specifically, during interglacial phases, when the ice melted and new habitats became suitable again, species could recolonize regions that were previously covered by ice, such as high latitudes and elevations. Based on theoretical models and empirical data, a decrease in genetic variation is predicted along recolonization routes as a result of the consecutive founder effects that characterize the recolonization process. In the present study, we assessed the relative importance of historical and contemporary processes in shaping genetic diversity and differentiation of bank vole ( Myodes glareolus) populations at different elevations in the Swiss Alps. By contrast to expectations, we found that genetic variation increased with elevation. Estimates of recent migration rates and a contrasting pattern of genetic differentiation observed at the mitochondrial cytochrome b gene and nuclear microsatellites support the hypothesis that higher genetic diversity at high elevation results from contemporary gene flow. Although historical recolonization processes can have marked effects on the genetic structure of populations, the present study provides an example where contemporary processes along an environmental gradient can reverse predicted patterns of genetic variation. [ABSTRACT FROM AUTHOR]

The pleated ascidian Styela plicata (Lesueur, 1823) is a solitary species commonly found in ports and marinas around the world. It has been recorded in the Mediterranean region since the mid-19th century. In the present work, the species' genetic diversity was analysed, employing a 613-bp portion of the mitochondrial cytochrome c oxidase subunit I ( COI) gene from 149 individuals collected in 14 ports along Italian coasts at spatial scales ranging from 1 to approximately 2200 km. Haplotype and nucleotide diversity values were h = 0-0.933 (total h = 0.789) and π = 0-0.145 (total π = 0.0094), respectively. A general southward trend of increasing within-population genetic diversity was observed. Analysis of molecular variance revealed significant genetic structuring but no significant differences were detected among basins, and no isolation by distance was found. Our data were integrated with the COI sequences available from previous studies and re-analysed in order to investigate the possible routes of introduction of this ascidian into the Mediterranean Sea. The presence of the two COI haplogroups detected in previous molecular investigations on S. plicata at intercontinental spatial scale was confirmed in the Mediterranean Sea. The results revealed multiple introductions of S. plicata, although some locations appear to have experienced rapid expansion from few founding individuals with reduced genetic diversity. However, continuous introductions would confound the pattern deriving from single founder events and make it difficult to estimate the time needed for gene diffusion into established populations. This mixing of effects creates difficulties in understanding the past and current dynamics of this introduction, and managing this alien invasive ascidian whose genetic structure is continuously shuffled by vessel-mediated transport. [ABSTRACT FROM AUTHOR]

Aim The aim of this study was to resolve the evolutionary history, biogeographical barriers and population histories for sister species of wrasses, the African Coris ( Coris cuvieri) in the Indian Ocean and Red Sea, and the Yellowtail Coris ( Coris gaimard) in the Pacific Ocean. Glacial sea level fluctuations during the Pleistocene have shaped the evolutionary trajectories of Indo-Pacific marine fauna, primarily by creating barriers between the Red Sea, Indian Ocean and Pacific Ocean. Here, we evaluate the influence of these episodic glacial barriers on sister species C. cuvieri and C. gaimard. Location Red Sea, Indian Ocean, Pacific Ocean. Methods Sequences from mitochondrial DNA cytochrome oxidase c subunit I (COI), and nuclear introns gonadotropin-releasing hormone (GnRH) and ribosomal S7 protein were analysed in 426 individuals from across the range of both species. Median-joining networks, analysis of molecular variance and Bayesian estimates of the time since most recent common ancestor were used to resolve recent population history and connectivity. Results Cytochrome oxidase c subunit I haplotypes showed a divergence of 0.97% between species, and nuclear alleles were shared between species. No population structure was detected between the Indian Ocean and Red Sea. The strongest signal of population structure was in C. gaimard between the Hawaiian biogeographical province and other Pacific locations (COI ϕST = 0.040-0.173, P < 0.006; S7 ϕST = 0.046, P < 0.001; GnRH ϕST = 0.022, P < 0.005). Time to most recent common ancestor is c. 2.12 Ma for C. cuvieri and 1.76 Ma for C. gaimard. Main conclusions We demonstrate an Indian-Pacific divergence of < 2 Myr and high contemporary gene flow between the Red Sea and Indian Ocean, mediated in part by the long pelagic larval stage. The discovery of hybrids at Christmas Island indicates that Indian and Pacific lineages have come into secondary contact after allopatric isolation. Subspecies status may be appropriate for these two wrasses. [ABSTRACT FROM AUTHOR]

Aim This study compares the phylogeography, population structure and evolution of four butterflyfish species in the Chaetodon subgenus Corallochaetodon, with two widespread species (Indian Ocean - C. trifasciatus and Pacific Ocean - C. lunulatus), and two species that are largely restricted to the Red Sea ( C. austriacus) and north-western ( NW) Indian Ocean ( C. melapterus). Through extensive geographical coverage of these taxa, we seek to resolve patterns of genetic diversity within and between closely related butterflyfish species in order to illuminate biogeographical and evolutionary processes. Location Red Sea, Indian Ocean and Pacific Ocean. Methods A total of 632 individuals from 24 locations throughout the geographical ranges of all four members of the subgenus Corallochaetodon were sequenced using a 605 bp fragment (cytochrome b) of mt DNA. In addition, 10 microsatellite loci were used to assess population structure in the two widespread species. Results Phylogenetic reconstruction indicates that the Pacific Ocean C. lunulatus diverged from the Indian Ocean C. trifasciatus approximately 3 Ma, while C. melapterus and C. austriacus comprise a cluster of shared haplotypes derived from C. trifasciatus within the last 0.75 Myr. The Pacific C. lunulatus had significant population structure at peripheral locations on the eastern edge of its range (French Polynesia, Johnston Atoll, Hawai'i), and a strong break between two ecoregions of the Hawaiian Archipelago. The Indian Ocean C. trifasciatus showed significant structure only at the Chagos Archipelago in the central Indian Ocean, and the two range-restricted species showed no population structure but evidence of recent population expansion. Main conclusions Patterns of endemism and genetic diversity in Corallochaetodon butterflyfishes have been shaped by (1) Plio-Pleistocene sea level changes that facilitated evolutionary divergences at biogeographical barriers between Indian and Pacific Oceans, and the Indian Ocean and Red Sea, and (2) semi-permeable oceanographic and ecological barriers working on a shorter time-scale. The evolution of range-restricted species (Red Sea and NW Indian Ocean) and isolated populations (Hawai'i) at peripheral biogeographical provinces indicates that these areas are evolutionary incubators for reef fishes. [ABSTRACT FROM AUTHOR]

The history of domestic sheep ( Ovis aries) in Africa remains largely unknown. After being first introduced from the Near East, sheep gradually spread through the African continent with pastoral societies. The eastern part of Africa was important either for the first diffusion of sheep southward or for putative secondary introductions from the Arabian Peninsula or southern Asia. We analysed mitochondrial DNA control region sequences of 91 domestic sheep from Kenya and found a high diversity of matrilines from the widespread haplogroup B, whereas only a single individual from haplogroup A was detected. Our phylogeography analyses of more than 500 available mitochondrial DNA sequences also identified ancestral haplotypes that were probably first introduced in Africa and are now widely distributed. Moreover, we found no evidence of an admixture between East and West African sheep. The presence of shared haplotypes in eastern and ancient southern African sheep suggests the possible southward movement of sheep along the eastern part of Africa. Finally, we found no evidence of an extensive introduction of sheep from southern Asia into Africa via the Indian Ocean trade. The overall findings on the phylogeography of East African domestic sheep set the grounds for understanding the origin and subsequent movements of sheep in Africa. The richness of maternal lineages in Kenyan breeds is of prime importance for future conservation and breeding programmes. [ABSTRACT FROM AUTHOR]

Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200-year-old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813-1861) was strongly reduced in descendants (1923-1940) during the mid-19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant-sized (managed) population. Differentiation was high among periods ( FST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mt DNA (D-loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population. [ABSTRACT FROM AUTHOR]

Aim To resolve phylogeographical partitions in the pronghorn spiny lobster, Panulirus penicillatus, which has a nine-month pelagic larval phase and the broadest distribution among spiny lobsters. With samples from the Red Sea to the East Pacific, we test genetic partitions across two-thirds of the planet, in a species with one of the longest pelagic phases. Location Red Sea, Indian and Pacific Oceans. Methods A fragment of the mt DNA cytochrome c oxidase subunit I gene ( COI) was resolved in 774 individuals from 28 locations, plus 55 sequences (10 locations) from public databases. Portions of COI, 12S and 16S mt DNA regions were resolved for phylogenetic analyses on a subset of individuals. Phylogenetic and population-level analyses were used to detect evolutionary partitions and dispersal barriers. Results Significant population structuring was detected (overall ΦST = 0.310, P < 0.001). Samples from the Red Sea and East Pacific Provinces (western and eastern range edges) comprise distinct phylogenetic lineages, divergent at d = 1.1% and 1.8%, respectively, from the Indo-Pacific. Coalescent analyses indicate a Pleistocene isolation for the Red Sea (0.71 Ma) and East Pacific (1.52 Ma). Excluding the Red Sea and East Pacific, structure across the rest of the range was comparatively low, but significant (ΦST = 0.018, P < 0.001). Main conclusions The Red Sea and East Pacific populations are phylogenetically distinct from populations elsewhere in the range. The East Pacific population diverged earliest, and may represent a distinct subspecies. Phylogeographical divisions align with the major Indo-Pacific biogeographical barriers, and with subsets of provincial designations from two frameworks: one based on levels of endemism and one on species composition. Tropical and temperate regions in the Pacific are significantly differentiated, potentially indicating an ecological partition. Isolation at eastern and western peripheral provinces may serve as a starting point for evolutionary diversification within this group. [ABSTRACT FROM AUTHOR]

The existence of two or more distinctly coloured phenotypes among individuals of an interbreeding population is known as colour polymorphism. In amphibians, this phenomenon is pervasive among anurans, but rare or absent among salamanders and caecilians, respectively. Here, we examine whether various distinct phenotypes of Salamandra salamandra in North Spain, used as a basis to describe the subspecies S. s. bernardezi and S. s. alfredschmidti, indeed warrant separate taxonomic status or that these co-occur and belong to a single taxon. Based on a sample of 1147 individuals from 27 local populations, six phenotype classes were designated. Although two phenotypes that are attributable to S. s. alfredschmidti show some degree of geographical restriction, these co-occur with those representing typical S. s. bernardezi. A fifth phenotype class could not be unambiguously attributed to either subspecies due to an overlap in previously suggested diagnostic characteristics. Mitochondrial (cytochrome b) and nuclear (β-fibrinogen) DNA analyses revealed S. s. alfredschmidti to be nested within several subclades of S. s. bernardezi, without displaying unique lineages. Furthermore, no significant divergence was recovered by means of niche overlap analyses. As a result, we revoke the subspecies status of S. s. alfredschmidti, which should be regarded as a junior synonym of S. s. bernardezi. The current findings confirm the existence of colour polymorphism in S. salamandra and the family Salamandridae, which provides exciting possibilities for future research. [ABSTRACT FROM AUTHOR]

To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mt DNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3-13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan. [ABSTRACT FROM AUTHOR]

The ancient acquisition of the mitochondrion into the ancestor of modern-day eukaryotes is thought to have been pivotal in facilitating the evolution of complex life. Mitochondria retain their own diminutive genome, with mitochondrial genes encoding core subunits involved in oxidative phosphorylation. Traditionally, it was assumed that there was little scope for genetic variation to accumulate and be maintained within the mitochondrial genome. However, in the past decade, mitochondrial genetic variation has been routinely tied to the expression of life-history traits such as fertility, development and longevity. To examine whether these broad-scale effects on life-history trait expression might ultimately find their root in mitochondrially mediated effects on core bioenergetic function, we measured the effects of genetic variation across twelve different mitochondrial haplotypes on respiratory capacity and mitochondrial quantity in the fruit fly, Drosophila melanogaster. We used strains of flies that differed only in their mitochondrial haplotype, and tested each sex separately at two different adult ages. Mitochondrial haplotypes affected both respiratory capacity and mitochondrial quantity. However, these effects were highly context-dependent, with the genetic effects contingent on both the sex and the age of the flies. These sex- and age-specific genetic effects are likely to resonate across the entire organismal life-history, providing insights into how mitochondrial genetic variation may contribute to sex-specific trajectories of life-history evolution. [ABSTRACT FROM AUTHOR]

Participating in the repair of nuclear DNA is one mechanism by which p53 suppresses tumorigenesis, but there is growing evidence that p53 also helps maintain the mitochondrial genome through its translocation into mitochondria and interactions with mt DNA repair proteins. Because of the susceptibility of mt DNA to oxidative damage and replication errors, it is vital to protect mt DNA genomic stability to preserve health and fitness. Here, we focus on reviewing the evidence for the involvement of p53 in maintaining the integrity of mt DNA through its activities in both the nucleus and the mitochondria. [ABSTRACT FROM AUTHOR]

A method was standardized to isolate quality DNA from cattle and buffalo fat for species identification using QIAamp DNA stool mini kit. The quality of the DNA was sufficient enough to amplify universal primers viz., mt 12S rRNA and mt 16S rRNA, and species specific D loop primers for cattle and buffalo. The sensitivity of the PCR assay in the species specific D loop primer amplification was with a detection level of 0. 47 ng cattle DNA and 0.23 ng buffalo DNA in simplex and, 0. 47 ng cattle DNA and 0.12 ng buffalo DNA in duplex PCR. It is a potentially reliable method for DNA detection to authenticate animal fat. [ABSTRACT FROM AUTHOR]

The identification and evaluation of the ecological and environmental factors shaping patterns of natural genetic variation are fundamental goals of population and conservation genetics. Many studies focus on factors affecting single species, but it is also important to test whether some influential biotic and abiotic factors are common drivers of genetic diversity across species, or if species or species groups are each affected by different forces; a multi-species analysis is necessary for this. Here we analysed the molecular variation from five mammal species (roe deer, red deer, chamois, mountain hare and European brown hare) at mt DNA and microsatellite loci from the eastern Italian Alps. We use phylogeographical and landscape-level analyses to test the relative influence of large-scale geographical history and contemporary environmental characteristics of the landscape on genetic diversity and differentiation. We found: (1) all study species except brown hare are strongly differentiated into two main groups, located west and east of a major river valley; (2) significant correlations between levels of within-population diversity at both mt DNA and microsatellite loci, and several landscape features such as alpine grassland, water courses and anthropized areas. We conclude that heterogeneous landscape has some influence on within-population diversity, but biogeographical history has probably had the stronger influence on current genetic patterns, despite an apparently large dispersal potential of certain species. However, our results for brown hare show that management actions such as stocking may alter these large-scale patterns. [ABSTRACT FROM AUTHOR]

An unknown taeniid cestode, resembling Taenia hydatigena, was recovered from a snow leopard, Uncia uncia in Mongolia. Morphology and nucleotide sequence of the mitochondrial cytochromec oxidase subunit 1 gene (mt DNA COI) ofthe cestode found was examined. The cestode is differed from T hydatigena both morphologically and genetically. The differences between two species were in the gross length, different number of testes, presence of vaginal sphincter and in egg size. The nucleotide sequence of this cestode differed from that of 7: hydatigena at 34 of the 384 (8.6%) nucleotide positions examined. The present cestode is very close to 7: kotlani in morphology and size of rostellar hooks. However, the adult stages of the latter species are unknown, and further comparison was unfeasible.

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene ( cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts. [ABSTRACT FROM AUTHOR]