Mitochondrial DNA phylogeography of Spodoptera exigua across a broad geographic area in China

The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae), is an important agriculture pest in China that causes serious economic losses in some of the main crop‐producing areas. To monitor and manage this pest effectively, it is necessary to investigate its phylogeographic patterns in China. In this study, we used a partial sequence of mitochondrial DNA Cytb gene consisting of 724 bps to investigate the genetic diversity of the beet armyworm. A total of 765 individuals from 47 populations across the main distribution range of the species were collected, and 112 haplotypes were identified. Moderate‐to‐high levels of genetic diversity (Hd = 0.672 ± 0.017, Pi = 0.00268 ± 0.00021) for the total populations were obtained. Phylogenetic and median‐joining network analyses indicated there was no distinct geographic distribution pattern among haplotypes. Overall, the study also revealed significant differentiation among some populations (P < 0.05). The F_ST values of Shenyang population (SY2012–SY 2014), as well as Baoding (BD), Taian (TA), Lucheng (LC), Zhengzhou (ZZ) and Wuhan (WH), were significantly different from those of the populations in most other locations. Hierarchical AMOVA showed there was no significantly genetic structure between populations located in seven geographic regions and four main bioclimatic zones. Finally, unimodal mismatch distribution combined with negative Tajima's D (D = ?2.696, P < 0.001) and Fu's F_S (F_S = ?207.228, P > 0.05) indicated recent population expansion of S. exigua at large spatial scales in China.     

Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic

In Europe, southern peninsulas served as refugia during cold periods in the Pleistocene, acting both as centres of origin of endemisms and as sources from which formerly glaciated areas were recolonized during interglacial periods. Previous studies have revealed that within the main refugial areas, intraspecific lineages often survived in allopatric refugia. We analysed two mitochondrial markers (nad4, control region, approximately 1.4 kb) in 103 individuals representing the entire distribution of Lissotriton boscai, a newt endemic to the western Iberian Peninsula. We inferred the evolutionary history of the species through phylogenetic, phylogeographic and historical demographic analyses. The results revealed unexpected, deep levels of geographically structured genetic variability. We identified two main evolutionary lineages, each containing three well-supported clades. The first historical split involved populations from central-southwestern coastal Portugal and the ancestor of all the remaining populations around 5.8 million years ago. Both lineages were subsequently fragmented into different population groups between 2.5 and 1.2 million years ago. According to nested clade analysis, at lower hierarchical levels the patterns suggest restricted gene flow with isolation by distance, whereas at higher levels the clades exhibit signatures of contiguous range expansion. Bayesian Skyline Plots show recent bottlenecks, followed by demographic expansions in all lineages. The significant genetic structure found is consistent with long-term survival of populations in allopatric refugia, supporting the 'refugia-within-refugia' scenario for southern European peninsulas. The comparison of our results with other co-distributed species highlights the generality of this hypothesis for the Iberian herpetofauna and suggests that Mediterranean refuges had more relevance for the composition and distribution of present biodiversity patterns than currently acknowledged. We briefly discuss the taxonomic and conservation implications of our results.     

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.     

Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic

The northern Rocky Mountains have experienced a complex history of geological events and environmental fluctuation, including Pleistocene glaciation. To provide an initial assessment of the genetic impact of this history on the regional biota we estimated phylogenetic relationships within Tamias ruficaudus, a regional endemic, from cytochrome b sequence variation using parsimony, maximum likelihood, and nested clade analysis. Analyses of sequence variation in 187 individuals from 43 localities across the distribution of T. ruficaudus indicate a history of vicariance events and range fluctuation consistent with successive periods of extensive Pleistocene glaciation in the northern Rocky Mountains. Intraspecific divergence levels (c. 4.7% uncorrected) and phylogenetic structure are consistent with a genealogical vicariance initiated prior to the Late Pleistocene, whereas nested clade analyses indicate more recent population history structured by both fragmentation and range expansion. A comparison of sequence variation with bacular morphology indicates that the two genetically and morphologically differentiated entities exhibit a zone of differential character introgression. Sequence data support a multiple refugia hypothesis and provide a phylogeographical case study for the ongoing synthesis of regional biogeography for northern Rocky Mountain endemics.     

Microsatellite variation in autochthonous and introduced populations of the Alpine marmot (Marmota marmota) along a European west–east transect

Microsatellite variation was studied in 11 populations of the Alpine marmot along a west–east transect through the present distribution range. The samples represent five autochthonous and six introduced populations. Eleven loci were analysed in nine populations and six loci in the two populations from France. In the populations from the Western Alps, there is no indication for reduced variability as has been assumed in previous studies. However, a decrease of variation in the autochthonous populations was observed from the west to the east. The introduced populations showed a heterogeneous pattern reflecting the geographic origin of the released individuals. The population from the Spanish Pyrenees harbours a high level of variation and is genetically closest to the French populations. In Austria, three of the introduced populations have low variation and are closely related to the autochthonous populations from the western part of Austria. In contrast, two introduced populations from the central part of Austria are highly variable and resemble the populations from France. At least for one of these populations an early introduction of founder individuals from the Western Alps has been documented.     

Mitochondrial genome phylogeny reveals the deep-time origin of Gomphomastacinae (Orthoptera: Eumastacidae) and its alpine genera in China

Gomphomastacinae is a grasshopper subfamily in Eumastacidae, with a morphology and distribution distinct from other subfamilies. The alpine genera of Gomphomastacinae that inhabit the Qinghai–Tibet Plateau in China show unique characteristics adapted to high-altitude life. However, their phylogenetic position and biogeographic history remain controversial. Thus, to determine the diversification history of these alpine genera and the origin of the subfamily, we obtained mitochondrial genome sequences from all seven Gomphomastacinae genera distributed in China. The reconstructed phylogeny was well supported and confirmed the phylogenetic position of Gomphomastacinae within Eumastacidae. Time calibration revealed a deep-time origin of the subfamily dating back to the Cretaceous period, and the diversification among alpine genera was also an ancient pre-Miocene event (30–50 Ma). Based on phylogeny and time estimates, the most likely biogeographic scenario is that Gomphomastacinae originated from an ancestral lineage that lived in East Gondwana and dispersed to Central and Western Asia through India. Subsequently, the alpine genera likely diverged along with the uplift of the Qinghai–Tibet Plateau and survived drastic climate change by in situ adaptation to high-altitude dwellings.     

The Asian grass lizard (Takydromus sexlineatus) does not respond to the scent of a native mammalian predator

Lacertid lizards use chemical cues emitted by saurophagous snakes to evade predation. Whether these lizards can detect and respond to the chemical cues of predatory mammals has not been studied. As many mammals carry distinct body odours and/or use chemical cues for intraspecific communication, lizards can be expected to use these chemicals as early warning cues. To test this idea, we observed the behaviour of Asian grass lizards (Takydromus sexlineatus) that had been transferred to an unfamiliar test arena containing one of four scent treatments. No particular scent was applied to the arena in the control situation. Diluted aftershave served as a pungency control. In the snake treatment, scent of the Oriental whip snake (Ahaetulla prasina) was applied. We included this treatment to learn how Asian grass lizards react to predator chemical cues. Finally, in the mongoose treatment, the lizards were confronted with scent cues of several small Indian mongooses (Herpestes auropunctatus). Snake scent elicited foot shakes, startles and tail vibrations. These are behaviours that in lacertid lizards are associated with stressful situations such as predatory encounters. Surprisingly, lizards confronted with mongoose scent exhibited none of these stress-indicating behaviours. In fact, their behaviour did not differ from that of lizards subjected to an odourless control treatment. These results raise concern. Mongooses are rapidly invading ecosystems worldwide. If lizards that have co-evolved with mongooses are unable to detect these predators’ presence through chemical cues, it seems highly unlikely that evolutionary naïve lizards will develop this ability rapidly.     

Chloroplast DNA variation and phylogeography of Ligularia tongolensis (Asteraceae), a species endemic to the Hengduan Mountains region of China

In this research, we aimed to study the genetic variation and phylogeographic pattern of Ligularia tongolensis, a perennial herb endemic to the Hengduan Mountains region of China. We sequenced two chloroplast DNA (cpDNA) intergenic spacers (trnQ-5 rps16, trnL-rpl32) in 140 individuals from 14 populations of three groups (Jinshajiang vs. Yalongjiang vs. Wumeng) within this species range. High levels of haplotype diversity (Hd = 0.814) and total genetic diversity (Ht = 0.862) were detected at the species leve...     

Molecular phylogeography of four endemic Sagittaria species (Alismataceae) in the Sino‐Japanese Floristic Region of East Asia

To reveal the role of climate oscillations of the Quaternary in forming the contemporary plant diversity in the temperate Sino‐Japanese Floristic Region of mainland China, we assess the phylogeographical patterns of four Sagittaria species in the region using sequence data from plastid DNA non‐coding regions (psbA‐trnH, the rpl16 intron and trnC‐ycf6) and the internal transcribed spacers of nuclear ribosomal DNA (nrITS). Based on both datasets, the divergence time among the four studied species was estimated to fall in the Late Tertiary (plastid DNA: 7.1–13.7 Mya; ITS: 11.1–16.1 Mya). The ancestral distribution analyses revealed that regions with a great diversity in topography, climate and ecological conditions, e.g. the Hengduan Mountains, Central China and East China, were the areas where the endemics originated. Mismatch distribution analyses revealed that each species had experienced a range expansion in response to Quaternary climatic oscillations. Our findings contradict the hypothesis of Quaternary origins of the endemic Sagittaria spp.; we support the view that modern species in the Northern Hemisphere originated mostly during the Tertiary. Range expansion may have profoundly modified the current distribution ranges of Sagittaria species in the Sino‐Japanese Floristic Region. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 6–20.     

Mitochondrial DNA variation and population structure of the island endemic Azorean bat (Nyctalus azoreum)

The Azorean bat Nyctalus azoreum is the only endemic mammal native to the remote archipelago of the Azores. It evolved from a continental ancestor related to the Leisler's bat Nyctalus leisleri and is considered threatened because of its restricted and highly fragmented distribution. We studied the genetic variability in 159 individuals from 14 colonies sampled throughout the archipelago. Sequences of the D-loop region revealed moderate but highly structured genetic variability. Half of the 15 distinct haplotypes were restricted to a single island, but the most common was found throughout the archipelago, suggesting a single colonization event followed by limited interisland female gene flow. All N. azoreum haplotypes were closely related and formed a star-like structure typical of expanded populations. The inferred age of demographic expansions was consistent with the arrival of founder animals during the Holocene, well before the first humans inhabited the Azores. Comparisons with a population of N. leisleri from continental Portugal confirmed not only that all N. azoreum lineages were unique to the archipelago, but also that the current levels of genetic diversity were surprisingly high for an insular species. Our data imply that the Azorean bat has a high conservation value. We argue that geographical patterns of genetic structuring indicate the existence of two management units.     

Mitochondrial DNA phylogeography and population history of Meladema diving beetles on the Atlantic Islands and in the Mediterranean basin (Coleoptera,Dytiscidae)

The phylogeny and population history of Meladema diving beetles (Coleoptera, Dytiscidae) were examined using mitochondrial DNA sequence from 16S ribosomal RNA and cytochrome oxidase I genes in 51 individuals from 22 populations of the three extant species (M. imbricata endemic to the western Canary Islands, M. lanio endemic to Madeira and M. coriacea widespread in the Western Mediterranean and on the western Canaries), using a combination of phylogenetic and nested clade analyses. Four main lineages are observed within Meladema, representing the three recognized species plus Corsican populations of M. coriacea. Phylogenetic analyses demonstrate the sister relationship of the two Atlantic Island taxa, and suggest the possible paraphyly of M. coriacea. A molecular clock approach reveals that speciation within the genus occurred in the Early Pleistocene, indicating that the Atlantic Island endemics are not Tertiary relict taxa as had been proposed previously. Our results point to past population bottlenecks in all four lineages, with recent (Late-Middle Pleistocene) range expansion in non-Corsican M. coriacea and M. imbricata. Within the Canary Islands, M. imbricata seems to have independently colonized La Gomera and La Palma from Tenerife (although a colonization of La Palma from La Gomera cannot be discarded), and M. coriacea has independently colonized Tenerife and Gran Canaria from separate mainland lineages. In the Mediterranean basin this species apparently colonized Corsica on a single occasion, relatively early in its evolutionary history (Early Pleistocene), and has colonized Mallorca recently on multiple occasions. On the only island where M. coriacea and M. imbricata are broadly sympatric (Tenerife), we report evidence of bidirectional hybridization between the two species.     

Late Pleistocene speciation of three closely related tree peonies endemic to the Qinling–Daba Mountains,a major glacial refugium in Central China

Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China.     

Evolutionary response to Quaternary climate aridification and oscillations in north‐western China revealed by chloroplast phylogeography of the desert shrub Nitraria sphaerocarpa (Nitrariaceae)

To investigate the influence of climate aridification and oscillations on the genetic diversity and evolutionary processes of organisms in the Quaternary in north‐western China, we selected Nitraria sphaerocarpa and examined the phylogeographical structure and response to historical and environmental factors in populations of this species across most of its covered range. We found twelve haplotypes on the basis of two chloroplast DNA sequences (trnH‐psbA and rpl32‐trnL). The drying climate during the Quaternary is proposed to have been a driver for significant genetic isolation and divergence among populations in N. sphaerocarpa. Except for the sharing of haplotype D between the Hami Basin and Hexi Corridor, as well as of haplotype F between the Hexi Corridor and Alxa Desert, network analysis showed haplotypes to be almost completely different from region to region. Analysis of molecular variance indicated that genetic variation primarily occurred among populations and among nine geographical groups that were distinguished by spatial analysis of molecular variance, and a Mantel test showed that the correlation between genetic and geographical distances was significant. On the other hand, there was evidence for the occurrence of an episode of more favourable conditions in some regions. Geographical range expansion of two groups of N. sphaerocarpa populations was supported by significant values for Fu's F_S and unimodel mismatch distributions. During the last interglacial period, a warmer and wetter climate contributed to range expansion within portions of the Hexi Corridor. By contrast, based on ecological niche modelling, N. sphaerocarpa was indicated to have had a shrunken and more fragmented range during the Last Glacial Maximum. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 757–770.     

Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera,Podarcis pityusensis (Squamata: Lacertidae)

Two monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time‐calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This suggests a mid‐late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089–0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present‐day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.     

Mitochondrial DNA genome evidence for the existence of a third divergent lineage in the western Atlantic Ocean for the bull shark (Carcharhinus leucas)

We report for the first time a highly divergent lineage in the Caribbean Sea for the bull shark (Carcharhinus leucas) based on the analysis of 51 mitochondrial DNA genomes of individuals collected in the western North Atlantic. When comparing the mtDNA control region obtained from the mitogenomes to sequences reported previously for Brazil, the Caribbean lineage remained highly divergent. These results support the existence of a discrete population in Central America due to a phylogeographic break separating the Caribbean Sea from the western North Atlantic, Gulf of Mexico and South America.     

Genetic Identification of Grey Mullet Species (Mugilidae) by Analysis of Mitochondrial DNA Sequence: Application to Identify the Origin of Processed Ovary Products (Bottarga)

Mitochondrial DNA sequencing was used to identify and distinguish four species of commercially important Mediterranean grey mullets. Partial cytochrome b and D-loop sequences were obtained from the four fish species, and these were used to perform phylogenetic analysis and to determine species-specific DNA fingerprints. Species-specific amplification primers were designed from these fingerprints, and these were used to characterize the species origin of several samples of commercial, processed mullet ovary products. In addition to differentiating between food products from different species, this method is also sensitive enough to distinguish food products from mullets of the same species from different regions.     

Evolutionary processes in a continental island system: molecular phylogeography of the Aegean Nigella arvensis alliance (Ranunculaceae) inferred from chloroplast DNA

Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of past fragmentation, dispersal, and genetic drift on taxon diversification. We used phylogeographical (nested clade) and population genetic analyses to elucidate the relative roles of these processes in the evolutionary history of the Aegean Nigella arvensis alliance (= 'coenospecies'). We surveyed chloroplast DNA (cpDNA) variation in 455 individuals from 47 populations (nine taxa) of the alliance throughout its core range in the Aegean Archipelago and surrounding mainland areas of Greece and Turkey. The study revealed the presence of three major lineages, with largely nonoverlapping distributions in the Western, Central, and Eastern Aegean. There is evidence supporting the idea that these major lineages evolved in situ from a widespread (pan-Aegean) ancestral stock as a result of multiple fragmentation events, possibly due to the influence of post-Messinian sea flooding, Pleistocene eustatic changes and corresponding climate fluctuations. Over-sea dispersal and founder events appear to have played a rather insignificant role in the group's history. Rather, all analytical approaches identified the alliance as an organism group with poor seed dispersal capabilities and a susceptibility to genetic drift. In particular, we inferred that the observed level of cpDNA differentiation between Kikladian island populations of Nigella degenii largely reflects population history, (viz. Holocene island fragmentation) and genetic drift in the near absence of seed flow since their time of common ancestry. Overall, our cpDNA data for the N. arvensis alliance in general, and N. degenii in particular, indicate that historical events were important in determining the phylogeographical patterns seen, and that genetic drift has historically been relatively more influential on population structure than has cytoplasmic gene flow.     

Mitochondrial DNA sequence variation and genetic stock structure of Atlantic cod (Gadus morhua) from bay and offshore locations on the Newfoundland continental shelf

Bay cod, Atlantic cod (Gadus morhua) that over-winter in the deep-water bays of northeastern Newfoundland, have historically been regarded as distinct in migration and spawning behaviour from offshore (Grand Bank) cod stocks. To investigate their genetic relationships, we determined the DNA sequence of a 307-base-pair portion of the mitochondrial cytochrome b gene for 236 adult cod taken from the waters off northeastern Newfoundland, including fish found over-wintering and spawning in Trinity Bay. Although 17 genotypes were found, a single common genotype occurs at a frequency of greater than 80% in all samples, and no alternative genotype occurs at a frequency of greater than 3%. Genotype proportions did not differ significantly among samples. Measures of genetic subdivision among sampling locations are nil. Cod over-wintering in Trinity Bay are not genetically distinct from offshore cod. In combination with tagging and physiological studies, these data suggest that there is sufficient movement of cod between bay and offshore locations to prevent the development or maintenance of independent inshore stocks. Adult cod that over-winter in Trinity Bay appear to represent an assemblage of temporarily nonmigratory fish that have become physiologically acclimated to cold-water inshore environments. The pattern of genetic variation in northern cod suggests a recent population structure characterized by extensive movement of contemporary individuals superimposed on an older structure characterized by a bottleneck in the population size of cod in the north-western Atlantic.     

Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) — the influence of Quaternary climatic oscillations on population dispersion and divergence

The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse Onychomys leucogaster were examined using populations from a postulated area of endemism that includes three arid regions (Colorado Plateaus, Interior Plains, and Wyoming Basins) in western North America. Fifteen tetra- and heptanucleotide restriction enzymes were used to assay restriction-site variation in a 2150-bp PCR-amplified fragment of mtDNA representing the ND2 and part of the COI gene regions. A total of 18 mtDNA haplotypes were detected. Although overall genetic divergence among these haplotypes was low (average = 1.1%), phylogeographic structuring was apparent. Notably, a clear phylogenetic split separated one group of haplotypes restricted to the Wyoming Basins from all others. This phylogenetic split was further corroborated by examination of nucleotide sequence variation from a 270-bp stretch of the mtDNA cytochrome b gene. Overall geographic and phylogenetic patterns suggest a complex history of geographic structuring and subsequent mixing of populations of grasshopper mice throughout the late Pleistocene. These patterns of variation are evaluated relative to alternative hypotheses about biotic responses to Quaternary climatic oscillations in western North American arid regions.