Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

Complete mitochondrial genome of critically endangered catfish Hemibagrus punctatus (Jerdon, 1849) and comparative analysis for insights into the phylogeny of hemibagrids through mitogenomic approach

BACKGROUND

Hemibagrus punctatus (Jerdon, 1849) is a critically endangered bagrid catfish endemic to the Western Ghats of India, whose population is declining due to anthropogenic activities. The current study aims to compare the mitogenome of H. punctatus with that of other Bagrid catfishes and provide insights into their evolutionary relationships.

METHODS AND RESULTS

Samples were collected from Hemmige Karnataka, India. In the present study, the mitogenome of H. punctatus was successfully assembled, and its phylogenetic relationships with other Bagridae species were studied. The total genomic DNA of samples was extracted following the phenol-chloroform isoamyl alcohol method. Samples were sequenced, and the Illumina paired-end reads were assembled to a contig length of 16,517 bp. The mitochondrial genome was annotated using MitoFish and MitoAnnotator (Iwasaki et al., 2013). A robust phylogenetic analysis employing NJ (Maximum composite likelihood) and ASAP methods supports the classification of H. punctatus within the Bagridae family, which validates the taxonomic status of this species. In conclusion, this research enriches our understanding of H. punctatus mitogenome, shedding light on its evolutionary dynamics within the Bagridae family and contributing to the broader knowledge of mitochondrial genes in the context of evolutionary biology.

CONCLUSIONS

The study's findings contribute to a better understanding of the mitogenome of H. punctatus and provide insights into the evolutionary relationships within other Hemibagrids.

Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Parrotfishes (Perciformes: Scaridae)

In order to investigate the molecular evolution of mitogenomes among the family Scaridae, the complete mitogenome sequences of twelve parrotfish species were determined and compared with those of seven other parrotfish species. The comparative analysis revealed that the general features and organization of the mitogenome were similar among the 19 parrotfish species. The base composition was similar among the parrotfishes, with the exception of the genus Calotomus, which exhibited an unusual negative AT skew in the whole mitogenome. The PCGs showed similar codon usage, and all of them underwent a strong purifying selection. The gene rearrangement typical of the parrotfishes was detected, with the tRNAMet inserted between the tRNAIle and tRNAGln, and the tRNAGln was followed by a putative tRNAMet pseudogene. The parrotfish mitogenomes displayed conserved gene overlaps and secondary structure in most tRNA genes, while the non-coding intergenic spacers varied among species. Phylogenetic analysis based on the thirteen PCGs and two rRNAs strongly supported the hypothesis that the parrotfishes could be subdivided into two clades with distinct ecological adaptations. The early divergence of the sea grass and coral reef clades occurred in the late Oligocene, probably related to the expansion of sea grass habitat. Later diversification within the coral reef clade could be dated back to the Miocene, likely associated with the geomorphology alternation since the closing of the Tethys Ocean. This work provided fundamental molecular data that will be useful for species identification, conservation, and further studies on the evolution of parrotfishes.

Consideration of genetic variation and evolutionary history in future conservation of Indian one-horned rhinoceros (Rhinoceros unicornis)

Background

The extant members of the Asian rhinos have experienced severe population and range declines since Pleistocene through a combination of natural and anthropogenic factors. The one-horned rhino is the only Asian species recovered from such conditions but most of the extant populations are reaching carrying capacity. India currently harbours ~ 83% of the global wild one-horned rhino populations distributed across seven protected areas. Recent assessments recommend reintroduction-based conservation approaches for the species, and implementation of such efforts would greatly benefit from detailed genetic assessments and evolutionary history of these populations. Using mitochondrial data, we investigated the phylogeography, divergence and demographic history of one-horned rhinos across its Indian range.

Results

We report the first complete mitogenome from all the extant Indian wild one-horned rhino populations (n = 16 individuals). Further, we identified all polymorphic sites and assessed rhino phylogeography (2531 bp mtDNA, n = 111 individuals) across India. Results showed 30 haplotypes distributed as three distinct genetic clades (F_st value 0.68–1) corresponding to the states of Assam (n = 28 haplotypes), West Bengal and Uttar Pradesh (both monomorphic). The reintroduced population of Uttar Pradesh showed maternal signatures of Chitwan National Park, Nepal. Mitochondrial phylogenomics suggests one-horned rhino diverged from its recent common ancestors ~ 950 Kya and different populations (Assam, West Bengal and Uttar Pradesh/Nepal) coalesce at ~ 190–50 Kya, corroborating with the paleobiogeography history of the Indian subcontinent. Further, the demography analyses indicated historical decline in female effective population size ~ 300–200 Kya followed by increasing trends during ~ 110–60 Kya.

Conclusion

The phylogeography and phylogenomic outcomes suggest recognition of three ‘Evolutionary Significant Units (ESUs)’ in Indian rhino. With ongoing genetic isolation of the current populations, future management efforts should focus on identifying genetically variable founder animals and consider periodic supplementation events while planning future rhino reintroduction programs in India. Such well-informed, multidisciplinary approach will be the only way to ensure evolutionary, ecological and demographic stability of the species across its range.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02045-2.

Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)

Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.

Complete mitogenomes reveal limited genetic variability in the garden dormouse Eliomys quercinus of the Iberian Peninsula

The garden dormouse Eliomys quercinus is a poorly known Western Palearctic species experiencing a global decline. Even though the availability of genetic information is key to assess the driversunderlying demographic changes in wild populations and plan adequate management, data on E. quercinus are still scant. In this study, we reconstructed the complete mitogenomes of four E. quercinus individuals from southern Spain using in–solution enriched libraries, and found evidence of limited genetic variability. We then compared their cytochrome b sequences to those of conspecifics from other countries and supported the divergent but genetically depauperate position of this evolutionarily significant unit (ESU). The information produced will assist future conservation studies on this little–studied rodent.

Discordance in maternal and paternal genetic markers in lesser long-nosed bat Leptonycteris yerbabuenae, a migratory bat: recent expansion to the North and male phylopatry

Leptonycteris yerbabuenae, the lesser long-nosed bat is an abundant migratory nectar-feeding bat found in most of Mexico, and in some areas of northern Central America and small sections of southwestern USA. We analyzed the distribution of the maternal and paternal lineages of this species with phylogeographic methods based on two mitochondrial markers, Cyt-b and D-loop, and a marker located in the Y chromosome, DBY. We obtained tissue samples from 220 individuals from 23 localities. Levels of genetic diversity (haplotype diversity, Hd ) were high (Cyt-b = 0.757; D-loop = 0.8082; DBY = 0.9137). No clear patterns of population genetic structure were found for mitochondrial markers, while male genetic differentiation suggested the presence of two lineages: one from Mexican Pacific coast states and another from central-southern Mexico; in accordance to strong male philopatry and higher female migration. We used genealogical reconstructions based on Bayesian tools to calculate divergence times, and to test coalescent models to explain changes in L. yerbabuenae historical demography. Our results show that recent demographic changes were consistent with global climatic changes (∼130,000 kyr ago for Cyt-b and ∼160,000 kyr for D-loop) and divergence times dated from molecular genealogies exhibited older divergence times, Cyt-b (4.03 mya), D-loop (10.26 mya) and DBY (12.23 mya). Accordingly, the female lineage underwent demographic expansion associated to Pleistocene climate change, whereas the male lineage remained constant.

Landscape of stress: Tree mortality influences physiological stress and survival in a native mesocarnivore

Climate change and anthropogenic modifications to the landscape can have both positive and negative effects on an animal. Linking landscape change to physiological stress and fitness of an animal is a fundamental tenet to be examined in applied ecology. Cortisol is a glucocorticoid hormone that can be used to indicate an animal's physiological stress response. In the Sierra Nevada Mountains of California, fishers (Pekania pennanti) are a threatened mesocarnivore that have been subjected to rapid landscape changes due to anthropogenic modifications and tree mortality related to a 4-year drought. We measured cortisol concentrations in the hair of 64 fishers (41 females, 23 males) captured and radio-collared in the Sierra National Forest, California. We addressed two main questions: (1) Is the physiological stress response of fishers influenced by anthropogenic factors, habitat type, canopy cover, and tree mortality due to drought in their home range? (2) Does the physiological stress response influence survival, reproduction, or body condition? We examined these factors within a fisher home range at 3 scales (30, 60, 95% isopleths). Using model selection, we found that tree mortality was the principle driver influencing stress levels among individual fishers with female and male fishers having increasing cortisol levels in home ranges with increasing tree mortality. Most importantly, we also found a link between physiological stress and demography where female fishers with low cortisol levels had the highest annual survival rate (0.94), whereas females with medium and high cortisol had lower annual survival rates, 0.78 and 0.81, respectively. We found no significant relationships between cortisol levels and body condition, male survival, or litter size. We concluded that tree mortality related to a 4-year drought has created a "landscape of stress" for this small, isolated fisher population.

Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone

We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina)

The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48-3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.

Landscape use by fishers (Pekania pennanti): core areas differ in habitat than the entire home range

Home ranges have long been studied in animal ecology. Core areas may be used at a greater proportion than the rest of the home range, implying the core contains dependable resources. The Pacific fisher (Pekania pennanti (Erxleben, 1777)) is a rare mesocarnivore occupying a small area in the Sierra Nevada Mountains, California, USA. Once statewide, fishers declined in the 1900s due to trapping, habitat fragmentation, and development. Recently, drought induced by climate change may be affecting this population. We examined space use of fishers in their core versus their home range for levels of anthropogenic modifications (housing density, road density, silvicultural treatments), habitat types, and tree mortality. We found core areas contained more late-successional forest and minimal human activity compared with their territory. Their core had higher levels of dense canopy and higher amounts of conifer cover, while minimizing the amount of buildings, developed habitat, and low canopy cover. Fishers may in effect be seeking refugia by minimizing their exposure to these elements in their core. Conserving landscape components used by fishers in their core areas will be important for the persistence of this isolated population.

Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages

The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species-Leptogorgia virgulata and Leptogorgia hebes-from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil-calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.

Phylogeography of moose in western North America

Subspecies designations within temperate species’ ranges often reflect populations that were isolated by past continental glaciation, and glacial vicariance is believed to be a primary mechanism behind the diversification of several subspecies of North American cervids. We used genetics and the fossil record to study the phylogeography of three moose subspecies (Alces alces andersoni, A. a. gigas, and A. a. shirasi) in western North America. We sequenced the complete mitochondrial genome (16,341 base pairs; n = 60 moose) and genotyped 13 nuclear microsatellites (n = 253) to evaluate genetic variation among moose samples. We also reviewed the fossil record for detections of all North American cervids to comparatively assess the evidence for the existence of a southern refugial population of moose corresponding to A. a. shirasi during the last glacial maximum of the Pleistocene. Analysis of mtDNA molecular variance did not support distinct clades of moose corresponding to currently recognized subspecies, and mitogenomic haplotype phylogenies did not consistently distinguish individuals according to subspecies groupings. Analysis of population structure using microsatellite loci showed support for two to five clusters of moose, including the consistent distinction of a southern group of moose within the range of A. a. shirasi. We hypothesize that these microsatellite results reflect recent, not deep, divergence and may be confounded by a significant effect of geographic distance on gene flow across the region. Review of the fossil record showed no evidence of moose south of the Wisconsin ice age glaciers ≥ 15,000 years ago. We encourage the integration of our results with complementary analyses of phenotype data, such as morphometrics, originally used to delineate moose subspecies, for further evaluation of subspecies designations for North American moose.

What does mitogenomics tell us about the evolutionary history of the Drosophila buzzatii cluster (repleta group)?

The Drosophila repleta group is an array of more than 100 species endemic to the “New World”, many of which are cactophilic. The ability to utilize decaying cactus tissues as breeding and feeding sites is a key aspect that allowed the successful diversification of the repleta group in American deserts and arid lands. Within this group, the Drosophila buzzatii cluster is a South American clade of seven closely related species in different stages of divergence, making them a valuable model system for evolutionary research. Substantial effort has been devoted to elucidating the phylogenetic relationships among members of the D. buzzatii cluster, including molecular phylogenetic studies that have generated ambiguous results where different tree topologies have resulted dependent on the kinds of molecular marker used. Even though mitochondrial DNA regions have become useful markers in evolutionary biology and population genetics, none of the more than twenty Drosophila mitogenomes assembled so far includes this cluster. Here, we report the assembly of six complete mitogenomes of five species: D. antonietae, D. borborema, D. buzzatii, two strains of D. koepferae and D. seriema, with the aim of revisiting phylogenetic relationships and divergence times by means of mitogenomic analyses. Our recovered topology using complete mitogenomes supports the hypothesis of monophyly of the D. buzzatii cluster and shows two main clades, one including D. buzzatii and D. koepferae (both strains), and the other containing the remaining species. These results are in agreement with previous reports based on a few mitochondrial and/or nuclear genes, but conflict with the results of a recent large-scale nuclear phylogeny, indicating that nuclear and mitochondrial genomes depict different evolutionary histories.

Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear

The cave bear (Ursus spelaeus) is one of the Late Pleistocene megafauna species that faced extinction at the end of the last ice age. Although it is represented by one of the largest fossil records in Europe and has been subject to several interdisciplinary studies including palaeogenetic research, its fate remains highly controversial. Here, we used a combination of hybridisation capture and next generation sequencing to reconstruct 59 new complete cave bear mitochondrial genomes (mtDNA) from 14 sites in Western, Central and Eastern Europe. In a Bayesian phylogenetic analysis, we compared them to 64 published cave bear mtDNA sequences to reconstruct the population dynamics and phylogeography during the Late Pleistocene. We found five major mitochondrial DNA lineages resulting in a noticeably more complex biogeography of the European lineages during the last 50,000 years than previously assumed. Furthermore, our calculated effective female population sizes suggest a drastic cave bear population decline starting around 40,000 years ago at the onset of the Aurignacian, coinciding with the spread of anatomically modern humans in Europe. Thus, our study supports a potential significant human role in the general extinction and local extirpation of the European cave bear and illuminates the fate of this megafauna species.

A survey of molecular diversity and population genetic structure in North American clearwing moths (Lepidoptera: Sesiidae) using cytochrome c oxidase I

The phylogeographic structure of insect species in North America is poorly understood. The moth family Sesiidae (Lepidoptera) contains many economically important pests of agriculture and forestry, as well as beneficial species used in biological control. Despite their significance, this study constitutes the first broad-ranging population genetic study on North American sesiids. It probes the population structure of eight species of sesiid moths based on sequence variation in cytochrome c oxidase I (N = 191). Haplotype diversity levels were high in seven of the eight species, while nucleotide diversity varied considerably. Patterns ranged from limited structure and a starburst pattern in the raspberry crown borer Pennisetia marginata to highly geographically structured populations in the peachtree borer Synanthedon exitiosa and the maple callus borer Synanthedon acerni. These varied patterns suggest differing evolutionary histories and dispersal abilities. By elucidating population genetic structure and barriers to dispersal we can begin to devise conservation and management plans.

Intraspecific mitogenomics of three marine species-at-risk: Atlantic, spotted, and northern wolffish (Anarhichas spp.)

High-resolution mitogenomics of within-species relationships can answer such phylogeographic questions as how species survived the most recent glaciation, as well as identify contemporary factors such as physical barriers, isolation, and gene flow. We examined the mitogenomic population structure of three at-risk species of wolffish: Atlantic (Anarhichas lupus), spotted (A. minor), and northern (A. denticulatus). These species are extensively sympatric across the North Atlantic but exhibit very different life history strategies, a combination that results in concordant and discordant patterns of genetic variation and structure. Wolffish haplogroups were not structured geographically: Atlantic and spotted wolffish each comprised three shallow clades, whereas northern wolffish comprised two deeper but unstructured lineages. We suggest that wolffish species survived in isolation in multiple glacial refugia, either refugia within refugia (Atlantic and spotted wolffish) or more distant refugia (northern wolffish), followed by secondary admixture upon post-glacial recolonisation of the North Atlantic.

Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations

The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High-resolution, whole-genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans-Atlantic comparisons (ΦST = .029-.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000-.060) or defined management stocks (ΦST = .000-.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans-Atlantic phylogeography versus absence of such structure within various partitions of trans-Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near-identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153-.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200-250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography

The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.

Genetic population structure of fishers (Pekania pennanti) in the Great Lakes region: remnants and reintroductions

Reintroduction programs have been pivotal in augmenting populations of fishers (Pekania pennanti (Erxleben, 1777)) and re-establishing them to their former range in North America. The majority of reintroduction efforts in fishers have been considered demographically successful, but reintroductions can alter genetic population structure and success has rarely been evaluated in fishers from a genetic standpoint. We used microsatellite data (n = 169) to examine genetic population structure of fishers in the Great Lakes region and comment on the success of past reintroductions at two different spatial scales. We found significant genetic population structure among source and reintroduced populations within the Great Lakes region and large-scale genetic structure between fisher populations located in two geographically distant regions (Great Lakes and Northeast) in the eastern United States. Reintroductions associated with the Great Lakes produced results that were largely consistent with other studies of fisher reintroductions in the Northeast. However, our data are the first to support a measurable impact on genetic population structure in Pekania pennanti pennanti (Erxleben, 1777) from a reintroduction using geographically distant source and reintroduced populations. When feasible, we strongly recommend that reintroduction programs include an investigation of the underlying genetic structure to better define intended goals and supplement measures of demographic success.

The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes

BACKGROUND

Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods.

RESULTS

Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration.

CONCLUSIONS

Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus Aratinga. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree.

Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida)

A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorphacoarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of Asiomorphacoarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.

Merging and comparing three mitochondrial markers for phylogenetic studies of Eurasian reindeer (Rangifer tarandus)

Phylogenetic analyses provide information that can be useful in the conservation of genetic variation by identifying intraspecific genetic structure. Reconstruction of phylogenetic relationships requires the use of markers with the appropriate amount of variation relative to the timeframe and purpose of the study. Here, genetic structure and clustering are inferred from comparative analyses of three widely used mitochondrial markers, the CR, cytb and the COI region, merged and separately, using Eurasian reindeer as a model. A Bayesian phylogeny and a MJ network, both based on the merged dataset, indicate several distinct maternal haplotype clusters within Eurasian reindeer. In addition to confirm previously described clusters, two new subclusters were found. When comparing the results from the merged dataset with the results from analyses of the three markers separately, similar clustering was found in the CR and COI phylogenies, whereas the cytb region showed poor resolution. Phylogenetic analyses of the merged dataset and the CR revealed congruent results, implying that single sequencing analysis of the CR is an applicable method for studying the haplotype structure in Eurasian reindeer.

Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Background

The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships.

Results

Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data.

Conclusions

The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0650-z) contains supplementary material, which is available to authorized users.

The complete mitochondrial genome of the Tibetan fox (Vulpes ferrilata) and implications for the phylogeny of Canidae

Canidae is a family of carnivores comprises about 36 extant species that have been defined as three distinct monophyletic groups based on multi-gene data sets. The Tibetan fox (Vulpes ferrilata) is a member of the family Canidae that is endemic to the Tibetan Plateau and has seldom been in the focus of phylogenetic analyses. To clarify the phylogenic relationship of V. ferrilata between other canids, we sequenced the mitochondrial genome and firstly attempted to clarify the relative phylogenetic position of V. ferrilata in canids using the complete mitochondrial genome data. The mitochondrial genome of the Tibetan fox was 16,667 bp, including 37 genes (13 protein-coding genes, 2 rRNA, and 22 tRNA) and a control region. A comparison analysis among the sequenced data of canids indicated that they shared a similar arrangement, codon usage, and other aspects. A phylogenetic analysis on the basis of the nearly complete mtDNA genomes of canids agreed with three monophyletic clades, and the Tibetan fox was highly supported as a sister group of the corsac fox within Vulpes. The estimation of the divergence time suggested a recent split between the Tibetan fox and the corsac fox and rapid evolution in canids. There was no genetic evidence for positive selection related to high-altitude adaption for the Tibetan fox in mtDNA and following studies should pay more attention to the detection of positive signals in nuclear genes involved in energy and oxygen metabolisms.

Survival of fishers in the southern Sierra Nevada region of California

Fishers in the western United States were recently proposed for listing under the U.S. Endangered Species Act because of concerns for loss of suitable habitat and evidence of a diversity of mortality risks that reduce survival. One of 2 remnant populations of fishers in California is in the southern Sierra Nevada region, where we studied them at 2 research sites in the Sierra National Forest. Our objectives were to evaluate whether survival was lower for male fishers and dispersal-aged individuals or if survival varied seasonally. We captured and monitored 232 radiocollared fishers from March 2007 to March 2014 and used model analyses to identify important predictors of survival. Fifty-two percent ( n = 120) of the radiocollared fishers died, and survival varied by sex and season, but not by age or between study sites. There was no evidence that dispersal-aged fishers experienced lower survival than older fishers. Annual survival trended lower for male (0.62 [95% CI 0.54–0.70]) compared to female fishers (0.72 [95% CI 0.67–0.78]), was lowest in the spring to mid-summer season (0.83 [95% CI 0.78–0.87]), and highest in late fall and winter (0.92 [95% CI 0.89–0.94]). Lower survival among male fishers appeared linked to males moving over large areas to locate mates, while lower survival for females was potentially related to high energetic cost of reproduction. It was possible but unknown if lower survival among all fishers in spring was linked to secondary exposure to toxicants dispersed around illicit marijuana grow sites. Six-month survival of juvenile fishers was 0.85 for females and 0.79 for males, but lower at 0.62 for females and 0.57 for males when adjusted for deaths before late September. Annual survival among adult female fishers was 20% lower than 0.90, a value that prior modeling suggested was required for population expansion in the overall southern Sierra Nevada. Survival data from our study imply a greater challenge for maintaining self-sustaining fisher populations in the southern Sierra Nevada region, and resource managers are working to mitigate several of the human-associated factors that limit population growth.

The mitochondrial genome of the peach fruit fly, Bactrocera zonata (Saunders) (Diptera: Tephritidae): Complete DNA sequence, genome organization, and phylogenetic analysis with other tephritids using next generation DNA sequencing

Mitochondrial genome can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. The complete 15,935 bp mitochondrial genome of Bactrocera zonata (Diptera: Tephritidae), is assembled from Illumina MiSeq read data. The mitogenome information for B. zonata was compared to the homologous sequences of other tephritids. Annotation indicated that the structure and orientation of 13 protein coding genes (PCGs), 22 tRNA and 2 rRNA sequences were typical of, and similar to, the ten closely related tephritid species. The nucleotide composition shows heavily biased toward As and Ts accounting 73.34% and exhibits a slightly positive AT skew, which is similar to other known tephritid species. All PCGs are initiated by ATN codons, except for cox1 with TCG and atp8 with GTG. Nine PCGs use a common stop codon of TAA or TAG, whereas the remaining four use an incomplete termination codon T or TA likely to be completed by adenylation. All tRNAs have the typical clover-leaf structure, with an exception for trnS((AGN)). Four short intergenic spacers showed high degree of conservation among B. zonata and other ten tephritids. A poly(T) stretch at the 5' end followed by [TA(A)]n-like stretch and a tandem repeats of 39 bp has been observed in CR. The analysis of gene evolutionary rate revealed that the cox1 and atp6 exhibits lowest and highest gene substitution rates, respectively than other genes. The phylogenetic relationships based on Maximum Likelihood method using all protein-coding genes and two ribosomal RNA genes confirmed that B. zonata is closely related to Bactrocera correcta, Bactrocera carambolae, Bactrocera papayae, and Bactrocera philippinensis and Bactrocera dorsalis belonging to B. dorsalis species complex forms a monophyletic clade, which is in accordance with the traditional morphological classification and recent molecular works.

Complete mitochondrial genome sequence of Ussurian moose, Alces alces cameloides

Ussurian moose (Alces alces cameloides) in Northeast China, which is on the southmost edge of the species' Eurasian range, are facing dramatic decline in population size and distribution areas. We undertook the first sequencing of the entire mitogenome of Ussurian moose, which is thought as the oldest moose subspecies to better understand the evolutionary history of this circumboreal sole extant species. The mitogenome is 16,418 bp in length, consisting of two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein-coding genes, and one control region. The overall base composition is A: 33.7%, T: 30.1%, C: 23.2%, and G: 13.0%, with a much higher A + T content. The phylogenetic tree of moose and 10 other most closely related Cervidae species was built.

Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing

Background

Mitochondrial DNA markers have long been used to identify population boundaries and are now a standard tool in conservation biology. In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with commonly used control region sequencing or other single gene approaches. In this study we sequenced the whole mitogenome of 93 Critically Endangered Speartooth Shark Glyphis glyphis from the last three river drainages they inhabit in northern Australia.

Results

Genetic diversity was extremely low (π =0.00019) but sufficient to demonstrate the existence of barriers to gene flow among river drainages (AMOVA Φ_ST =0.28283, P <0.00001). Surprisingly, the comparison with single gene sub-datasets revealed that ND5 and 12S were the only ones carrying enough information to detect similar levels of genetic structure. The control region exhibited only one mutation, which was not sufficient to detect any structure among river drainages.

Conclusions

This study strongly supports the use of single river drainages as discrete management units for the conservation of G. glyphis. Furthermore when genetic diversity is low, as is often the case in elasmobranchs, our results demonstrate a clear advantage of using the whole mitogenome to inform population structure compared to single gene approaches. More specifically, this study questions the extensive use of the control region as the preferential marker for elasmobranch population genetic studies and whole mitogenome sequencing will probably uncover a large amount of cryptic population structure in future studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0232-x) contains supplementary material, which is available to authorized users.

A mitogenomic phylogeny and genetic history of sable (Martes zibellina)

We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200-300 thousandyears ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~50-140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~23-50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka.

The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle

As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope may yield. Here, we increase the number of individuals and markers by an order of magnitude over previously published work to comprehensively assess the phylogeographical history of a well-studied declining species, the western pond turtle (Emys marmorata). We present a new analysis of 89 independent nuclear SNP markers and one mitochondrial gene sequence scored for rangewide sampling of >900 individuals, and compare these to smaller-scale, rangewide genetic and morphological analyses. Our enlarged SNP data fundamentally revise our understanding of evolutionary history for this lineage. Our results indicate that the gains from greatly increasing both the number of markers and individuals are substantial and worth the effort, particularly for species of high conservation concern such as the pond turtle, where accurate assessments of population history are a prerequisite for effective management.

Assembly and annotation of full mitochondrial genomes for the corn rootworm species, Diabrotica virgifera virgifera and Diabrotica barberi (Insecta: Coleoptera: Chrysomelidae), using Next Generation Sequence data

Complete mitochondrial genomes for two corn rootworm species, Diabrotica virgifera virgifera (16,747 bp) and Diabrotica barberi (16,632; Insecta: Coleoptera: Chrysomelidae), were assembled from Illumina HiSeq2000 read data. Annotation indicated that the order and orientation of 13 protein coding genes (PCGs), and 22 tRNA and 2 rRNA sequences were in typical of insect mitochondrial genomes. Non-standard nad4 and cox3 stop codons were composed of single T nucleotides and likely completed by adenylation, and atypical TTT start codons was predicted for both D. v. virgifera and D. barberinad1 genes. The D. v. virgifera and D. barberi haplotypes showed 819 variable nucleotide positions within PCG regions (7.36% divergence), which suggest that speciation may have occurred ~3.68 million years ago assuming a linear rate of short-term substitution. Phylogenetic analyses of Coleopteran MtD genome show clustering based on family level, and may have the capacity to resolve the evolutionary history within this Order of insects.

A long PCR-based approach for DNA enrichment prior to next-generation sequencing for systematic studies

PREMISE OF THE STUDY

We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing. Our approach can be used to generate templates from any DNA source for next-generation sequencing. Here we test our approach by amplifying complete chloroplast genomes, and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear and mitochondrial regions. •

METHODS AND RESULTS

Chloroplast genomes of 30 species across angiosperms were amplified to test our approach. Amplification success varied depending on whether PCR conditions were optimized for a given taxon. To further test our approach, some amplicons were sequenced on an Illumina HiSeq 2000. •

CONCLUSIONS

Although here we tested this approach by sequencing plastomes, long PCR amplicons could be generated using DNA from any genome, expanding the possibilities of this approach for molecular systematic studies.

A long PCR-based approach for DNA enrichment prior to next-generation sequencing for systematic studies

PREMISE OF THE STUDY

We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing. Our approach can be used to generate templates from any DNA source for next-generation sequencing. Here we test our approach by amplifying complete chloroplast genomes, and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear and mitochondrial regions. •

METHODS AND RESULTS

Chloroplast genomes of 30 species across angiosperms were amplified to test our approach. Amplification success varied depending on whether PCR conditions were optimized for a given taxon. To further test our approach, some amplicons were sequenced on an Illumina HiSeq 2000. •

CONCLUSIONS

Although here we tested this approach by sequencing plastomes, long PCR amplicons could be generated using DNA from any genome, expanding the possibilities of this approach for molecular systematic studies.

Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing

Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity.

Estimating Trend in Occupancy for the Southern Sierra Fisher Martes pennanti Population

Carnivores are important elements of biodiversity, not only because of their role in transferring energy and nutrients, but also because they influence the structure of the communities where they occur. The fisher Martes pennanti is a mammalian carnivore that is associated with late-successional mixed forests in the Sierra Nevada in California, and is vulnerable to the effects of forest management. As a candidate for endangered species status, it is important to monitor its population to determine whether actions to conserve it are successful. We implemented a monitoring program to estimate change in occupancy of fishers across a 12,240-km2 area in the southern Sierra Nevada. Sample units were about 4 km apart, consisting of six enclosed, baited track-plate stations, and aligned with the national Forest Inventory and Analysis grid. We report here the results of 8 y (2002–2009) of sampling of a core set of 223 sample units. We model the combined effects of probability of detection and occupancy to estimate occupancy, persistence rates, and trend in occupancy. In combined models, we evaluated four forms of detection probability (1-group and 2-group both constant and varying by year) and nine forms of probability of occupancy (differing primarily by how occupancy and persistence vary among years). The best-fitting model assumed constant probability of occupancy, constant persistence, and two detection groups (AIC weight  =  0.707). This fit the data best for the entire study area as well as two of the three distinct geographic zones therein. The one zone with a trend parameter found no significant difference from zero for that parameter. This suggests that, over the 8-y period, that there was no trend or statistically significant variations in occupancy. The overall probability of occupancy, adjusted to account for uncertain detection, was 0.367 (SE  =  0.033) and estimates were lowest in the southeastern zone (0.261) and highest in the southwestern zone (0.583). Constant and positive persistence values suggested that sample units rarely changed status from occupied to unoccupied or vice versa. The small population of fishers in the southern Sierra (probably &lt;250 individuals) does not appear to be decreasing. However, given the habitat degradation that has occurred in forests of the region, we favor continued monitoring to determine whether fisher occupancy increases as land managers implement measures to restore conditions favorable to fishers.