Length–weight relationships for Eutropiichthys murius (Hamilton, 1822), Coilia reynaldi Valenciennes, 1848 and Johnius gangeticus Talwar, 1991 from lower stretch of the River Ganga,India

Length‐weight relationships (LWRs) for three fish species from the River Ganga (India) is presented. Sampling was conducted from the lower stretch of the River Ganga (Patna: 25°36′51.66″N & 85°12′7.02″E to Freserganj: 21°35′40.58″N & 88°15′28.92″E) during April, June and September and December of 2017. Specimens were caught using gill nets (18 nos.; mesh 18–32 mm), and bag nets (3 nos.; mesh 14–22 mm). The values a and b from LWRs ‐were found to be 0.007 and 2.977 for Eutropiichthys murius; 0.003 and 3.001 for Coilia reynaldi; 0.009 and 3.010 for Johnius gangeticus.     

Mitochondrial genomes reveal mid-Pleistocene population divergence,and post-glacial expansion,in Australasian snapper (Chrysophrys auratus)

Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.Subject terms: Population genetics, Phylogenetics, Evolutionary genetics, Population genetics, Evolutionary biology     

Mitochondrial DNA in the Atlantic cod, Gadus morhua: lack of genetic divergence between eastern and western populations

Mitochondrial DNA variation was examined in two populations of Atlantic cod from the North Sea and the Grand Banks of Newfoundland. Eight restriction enzymes revealed no major genetic difference between these eastern and western populations. These results are discussed in relation to earlier electrophoretic studies on this species.     

Mitochondrial genes reveal cryptic diversity in plant-breeding frogs from Madagascar (Anura, Mantellidae, Guibemantis)

One group of mantellid frogs from Madagascar (subgenus Pandanusicola of Guibemantis) includes species that complete larval development in the water-filled leaf axils of rainforest plants. This group consists of six described species: G. albolineatus, G. bicalcaratus, G. flavobrunneus, G. liber, G. pulcher, and G. punctatus. We sequenced the 12S and 16S mitochondrial rRNA genes ( approximately 1.8 kb) from multiple specimens (35 total) of all six species to assess phylogenetic relationships within this group. All reconstructions strongly supported G. liber as part of the Pandanusicola clade, even though this species does not breed in plant leaf axils. This result confirms a striking reversal of reproductive specialization. However, all analyses also indicated that specimens assigned to G. liber include genetically distinct allopatric forms that do not form a monophyletic group. Most other taxa that were adequately sampled (G. bicalcaratus, G. flavobrunneus, and G. pulcher) likewise consist of several genetically distinct lineages that do not form monophyletic groups. These results suggest that many of the recognized species in this group are complexes of cryptic species.     

Leaf morphological and genetic divergence in populations of Drimys (Winteraceae) in Chile

The genus Drimys is distributed in Chile from semi-arid zones to sub-Antarctic forests; there are three species of this tree, D. andina, D. confertifolia and D. winteri, the latter with varieties chilensis and winteri. Northern populations are found in small disjunct natural refuges, specifically mountain cloud forests and the bottom of ravines. The size and continuity of populations are greater in the south, where wetter conditions prevail. Morphological differences between populations have been observed, particularly between the northern populations of Fray Jorge and Talinay. This observation, led to the following questions: a) what is the level of morphological and genetic divergence among the populations of Drimys in Chile? and b) do the populations from Fray Jorge/Talinay, currently classified as D. winteri var. chilensis, differ genetically from the other populations of this variety? To answer these questions, we collected leaf samples from 37 populations of all Chilean Drimys, performed leaf morphology analysis and estimated genetic divergence using RAPD markers. We found a high degree of leaf morphological and genetic divergence between the populations of Fray Jorge/Talinay and the other Chilean species of Drimys. The morphological and genetic divergence among varieties of D. winteri was greater than that among the species of Drimys, which may indicate problems with their taxonomic classification.     

Length–weight relationships of Hara hara (Hamilton, 1822), Pangio pangia (Hamilton, 1822) and Setipinna brevifilis (Valenciennes, 1848) from the lower Brahmaputra River,Northeast India

The present study describes the length–weight relationships (LWRs) for Hara hara, Pangio pangia and Setipinna brevifilis from the lower Brahmaputra River in Assam, Northeast India, collected from June 2016 to May 2017, using fishing gears namely cast nets (9′, 1 ⁄ 2″) and gillnets (30 × 0.9 m). No previous data have ever been recorded on LWR for these three species.     

High levels of genetic divergence and inbreeding in populations of cupuassu (Theobroma grandiflorum)

Theobroma grandiflorum (cupuassu) is an important fruit tree native to the Brazilian Amazon. Establishing the genetic diversity and structure of populations is critical to define long-term strategies for cupuassu conservation presently threatened by rapid deforestation. Three natural populations collected at the putative center of diversity, three groups of accessions established at a germplasm collection, and one derived from commercial plantings were analyzed. The genetic diversity was assessed using 21 polymorphic microsatellite loci originally developed for Theobroma cacao, disclosing a total of 113 alleles. The estimated genetic diversity parameters averaged over cupuassu populations (A = 3.53 alleles per locus; H _e = 0.426; H _o = 0.346) were lower than the values reported for other Neotropical tree species. The three natural populations presented a positive and significant fixation index (f), ranging from 0.133 to 0.234. Cupuassu apparently adhered to a general pattern of genetic diversity structure of some Neotropical tree species occurring at low densities, with a low intrapopulation genetic diversity and important levels of endogamy, possibly due to biparental inbreeding derived from the presence of spatial genetic structure in the populations. A high level of genetic divergence was detected among the natural populations (θ _p = 0.301), a strong differentiation caused by limited gene flow, and suggesting that human interference in spreading and/or stimulating plantings might have had a smaller effect than expected. The approximate location of the T. grandiflorum center of diversity could not be confirmed by analyzing natural populations from the putative region.     

High-quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)

The collembolan Folsomia candida Willem, 1902, is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal “standard” because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we obtained two high-quality chromosome-level genomes of F. candida, for a parthenogenetic strain (named FCDK, 219.08 Mb, 25,139 protein-coding genes) and a sexual strain (named FCSH, 153.09 Mb, 21,609 protein-coding genes), reannotated the genome of the parthenogenetic strain reported by Faddeeva-Vakhrusheva et al. in 2017 (named FCBL, 221.7 Mb, 25,980 protein-coding genes) and conducted comparative genomic analyses of the three strains. High genome similarities between FCDK and FCBL based on synteny, genome architecture, mitochondrial and nuclear gene sequences suggest that they are conspecific. The seven chromosomes of FCDK are each 25%–54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to the broader environmental adaptation of parthenogenetic strains. In addition, FCDK has fewer strain-specific microRNAs than FCSH, and their mitochondrial and nuclear genes have diverged greatly. In conclusion, FCDK/FCBL and FCSH have accumulated independent genetic changes and evolved into distinct species after 10 million years ago. Our work provides important genomic resources for studying the mechanisms of rapidly cryptic speciation and soil arthropod adaptation to soil ecosystems.     

Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains

Climate change during the Quaternary played an important role in the differentiation and evolution of plants. A prevailing hypothesis is that alpine and arctic species survived glacial periods in refugia at the periphery of glaciers. Though the Rocky Mountains, south of the southernmost extent of continental ice, served as an important glacial refuge, little is known about how climate cycles influenced populations within this region. We inferred the phylogeography of Sedum lanceolatum (Crassulaceae) within the Rocky Mountain refugium to assess how this high-elevation plant responded to glacial cycles. We sequenced 884 base pairs (bp) of cpDNA intergenic spacers (tRNA-L to tRNA-F and tRNA-S to tRNA-G) for 333 individuals from 18 alpine populations. Our highly variable markers allowed us to infer that populations persisted across the latitudinal range throughout the climate cycles, exhibited significant genetic structure, and experienced cycles of range expansion and fragmentation. Genetic differentiation in S. lanceolatum was most likely a product of short-distance elevational migration in response to climate change, low seed dispersal, and vegetative reproduction. To the extent that Sedum is a good model system, paleoclimatic cycles were probably a major factor preserving genetic variation and promoting divergence in high-elevation flora of the Rocky Mountains.     

Spatial genetic analyses reveal strong genetic structure in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae)

The development of spatial genetic structure (SGS) in seed plants has been linked to several biological attributes of species, such as breeding system and life form. However, little is known about SGS in ferns, which together with lycopods are unique among land plants in having two free‐living life stages. We combined spatial aggregation statistics and spatial genetic autocorrelation analyses using five plastid microsatellites and one nuclear gene to investigate SGS in two populations of the outcrossing tree fern Alsophila firma (Cyatheaceae). We assessed how the observed patterns compare with those estimated for other ferns and seed plants. Populations of A. firma exhibited strong SGS, spatial clustering of individuals, substantial clonal diversity and no inbreeding. SGS in ferns appears to be higher than in most seed plants analysed to date. Contrary to our expectations, an outcrossing breeding system, wind dispersal and an arborescent life form did not translate into weak or no SGS. In ferns, SGS is probably being affected by the life cycle with two free‐living life stages. The reproductive biology of ferns appears to be more complex than previously thought. This implies that SGS in ferns is affected by some factors that cannot be inferred from the study of flowering plants. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 439–449.     

Characterization of feeding habits,prey diversity and diet overlap of two sympatric species: Bronze catfish,Netuma bilineata (Valenciennes, 1840) and blacktip sea catfish,Plicofollis dussumieri (Valenciennes, 1840) in the northern Arabian Sea

This study describes the diet composition, diet overlap and prey diversity in two economically and ecologically important marine catfish species: the bronze catfish (Netuma bilineata) and the blacktip sea catfish (Plicofollis dussumieri) collected between January and December 2015 from the northern Arabian Sea coast of Pakistan. Stomach data of 342 bronze catfish and 283 blacktip sea catfish were examined. Diet composition and feeding strategy of each species by identification of stomach contents were weighed and enumerated. Both species primarily consumed teleosts, Brachyura and small amounts of a wide variety of prey items; however, specialization was a more common trait for the bronze catfish than for the black tip sea catfish. The Morisita‐Horn index showed considerable diet overlap in percentage of mean weights (0.847) than in numbers (0.612) between co‐prey pairs of both species. The highest Bray‐Curtis similarity between the southwest monsoon (SWM) and south inter monsoon (SIM) was observed in bronze catfish and lowest between autumn inter monsoon (AIM) seasons in both species. While Bray‐Curtis dissimilarity was observed, both species share diet niches and diet overlap. The present study evaluation of the feeding strategy and potential competition between two sympatric species of marine catfishes can provide the framework for their conservation and management in the region.     

Polymorphisms of mitochondrial ATPase 8/6 genes and association with milk production traits in holstein cows

The maternal effect has been widely proposed to affect the production traits in domestic animals. However, the sequence polymorphisms of mitochondrial DNA (mtDNA) and association with milk production traits in Holstein cows have remained unclear. In this study, we investigated the single nucleotide polymorphisms (SNPs) of mtDNA ATPase 8/6 genes and association with four milk production traits of interest in 303 Holstein cows. A total of 18 SNPs were detected among the 842?bp fragment of ATPase 8/6 genes, which determined six haplotypes of B. taurus (H1-H4) and B. indicus (H5-H6). The mixed model analysis revealed that there was significant association between haplotype and 305-day milk yield (MY). The highest MY was observed in haplotype H4. However, we did not detect statistically significant differences among haplotypes for the traits of milk fat (MF), milk protein (MP), and somatic cell count (SC). The overall haplotype diversity and nucleotide diversity of ATPase 8/6 genes were 0.563?±?0.030 and 0.00609?±?0.00043, respectively. The results suggested that mitochondrial ATPase 8/6 genes could be potentially used as molecular marker to genetically improve milk production in Holstein cows.     

Species trees,temporal divergence and historical biogeography of coastal rove beetles (Coleoptera: Staphylinidae) reveal their early Miocene origin and show that most divergence events occurred in the early Pliocene along the Pacific coasts

We investigated the species trees, temporal divergence and historical biogeography of Emplenota Casey and Triochara Bernhauer (ET clade hereafter), subgenera of the Aleochara coastal staphylinid beetles, to determine their place of origin. We explored a multilocus dataset to infer gene trees and species trees based on traditional concatenated and multispecies coalescent‐based approaches using both model‐ (maximum likelihood and Bayesian) and parsimony‐based methods. The multilocus dataset comprised DNA sequences from five nuclear genes (ArgK, CAD, EF1‐α, wg and 28S) and three mitochondrial genes (COI, COII and 16S). *BEAST analysis according to a coalescent‐based approach resolved the following phylogenetic relationships: ((A. trisulcata (A. nubis + A. zerchei)) (A. obscurella ((A. pacifica (A. curtidens + A. litoralis)) (A. hayamai (A. yamato (A. fucicola (A. segregata + A. puetzi))))))). Using a relaxed molecular clock, we reconstructed a time‐calibrated phylogeny for this group. Furthermore, to account for the historical biogeography of the ET clade at the ages of major divergences, we investigated the ancestral area based on a time‐calibrated phylogeny. Biogeographical analyses suggested that the ancestor of the ET clade was widely distributed along the eastern and western Palearctic and the western Nearctic coasts in the early Miocene. According to reconstruction of the ancestral area, one dispersal and three vicariance events were required, and the analyses indicated that vicariance events were important in shaping its current distribution patterns. Most of the divergence events occurred in the late Miocene and early Pliocene along the Pacific coasts, and the East Asian seacoasts harboured the most species‐rich fauna, including eight of the 13 species in the ET clade.     

Microsatellite markers reveal shallow genetic differentiation between cohorts of the common sea urchin Paracentrotus lividus (Lamarck) in northwest Mediterranean

Temporal variability was studied in the common sea urchin Paracentrotus lividus through the analysis of the genetic composition of three yearly cohorts sampled over two consecutive springs in a locality in northwestern Mediterranean. Individuals were aged using growth ring patterns observed in tests and samples were genotyped for five microsatellite loci. No reduction of genetic diversity was observed relative to a sample of the adult population from the same location or within cohorts across years. F _ST and amova results indicated that the differentiation between cohorts is rather shallow and not significant, as most variability is found within cohorts and within individuals. This mild differentiation translated into estimates of effective population size of 90–100 individuals. When the observed excess of homozygotes was taken into account, the estimate of the average number of breeders increased to c . 300 individuals. Given our restricted sampling area and the known small-scale heterogeneity in recruitment in this species, our results suggest that at stretches of a few kilometres of shoreline, large numbers of progenitors are likely to contribute to the larval pool at each reproduction event. Intercohort variation in our samples is six times smaller than spatial variation between adults of four localities in the western Mediterranean. Our results indicate that, notwithstanding the stochastic events that take place during the long planktonic phase and during the settlement and recruitment processes, reproductive success in this species is high enough to produce cohorts genetically diverse and with little differentiation between them. Further research is needed before the link between genetic structure and underlying physical and biological processes can be well established.     

Investigation on Mitochondrial tRNA<Superscript>Leu/Lys</Superscript>, NDI and ATPase 6/8 in Iranian Multiple Sclerosis Patients

As with chromosomal DNA, the mitochondrial DNA (mtDNA) can contain mutations that are highly pathogenic .In fact, many diseases of the central nervous system are known to be caused by mutations in mtDNA. Dysfunction of the mitochondrial Respiratory Chain (RC) has been shown in patients with neurological disease including Alzheimer’s disease (AD), Parkinson’s disease (PD) and Multiple sclerosis (MS). MS is a demyelinating disease of central nervous system characterized by morphological hallmarks of inflammation, demyelination and axonal loss. Considering this importance, we decided to investigate several highly mutative parts of mtDNA for point mutations as MT-LTI (tRNA^{Leucine1(UUA/G)}), MT-NDI (NADH Dehydrogenase subunit 1), MT-COII (Cytochrome c oxidase subunit II), MT-TK (tRNA^Lysine), MT-ATP8 (ATP synthase subunit F0 8) and MT-ATP6 (ATP synthase subunit F0 6) in 20 Iranian MS patients and 80 age-matched control subjects by PCR and automated DNA sequencing to evaluate any probable point mutations. Our results revealed that 15 (75%) out of 20 MS patients had point mutations. Some of point mutations were newly found in this study. This study suggested that point mutation occurred in mtDNA might be involved in pathogenesis of MS.     

Mitochondrial and nuclear sequence polymorphisms reveal geographic structuring in Amazonian populations of Echinococcus vogeli (Cestoda: Taeniidae)

To date, nothing is known about the genetic diversity of the Echinococcus neotropical species, Echinococcus vogeli and Echinococcus oligarthrus. Here we used mitochondrial and nuclear DNA sequence polymorphisms to uncover the genetic structure, transmission and history of E. vogeli in the Brazilian Amazon, based on a sample of 38 isolates obtained from human and wild animal hosts. We confirm that the parasite is partially synanthropic and show that its populations are diverse. Furthermore, significant geographical structuring is found, with western and eastern populations being genetically divergent.     

High genetic divergence characterizes populations of the endemic plant Lithophragma maximum (Saxifragaceae) on San Clemente Island

Narrowly-ranging species frequently harbor less genetic variability relative to widespread relatives and face graver extinction threats due to the heightened impacts of stochastic events on ecological and genetic diversity. In this study, we examined the impact of historical and current threats to the maintenance of genetic variation in Lithophragma maximum (Saxifragaceae), a perennial herb endemic to San Clemente Island, California. This species exists as small populations confined to canyons along 4 km of the southeast coastline of the island. In 15 populations analyzed with 10 microsatellite markers, we identified an average of 2.05 alleles per locus and 58.7% polymorphic loci. Significant departures from Hardy–Weinberg equilibrium existed in six populations; five of these exhibited heterozygote deficiency. Bayesian inference of genetic structure indicated a significant amount of structure among populations and canyons and infrequent gene flow even over very short distances. We also identified a significant and positive correlation between genetic and geographic distances, indicative of isolation by distance. There was no evidence of recent bottlenecks in any of the sampled populations, but older bottlenecks were detected in two populations. These results suggest that populations of L. maximum have historically been small and isolated, which is likely due to the rugged habitat in which this species occurs and limited pollen and seed dispersal. Given the high degree of structure observed across populations, we suggest that conservation efforts should focus on preserving populations in multiple canyons, maintaining large population sizes to preserve genetic variation, and controlling the spread of invasive species in areas where L. maximum occurs.