Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus)

African wild dogs are large, highly mobile carnivores that are known to disperse over considerable distances and are rare throughout much of their geographical range. Consequently, genetic variation within and differentiation between geographically separated populations is predicted to be minimal. We determined the genetic diversity of mitochondrial DNA (mtDNA) control region sequences and microsatellite loci in seven populations of African wild dogs. Analysis of mtDNA nucleotide diversity suggests that, historically, wild dog populations have been small relative to other large carnivores. However, population declines due to recent habitat loss have not caused a dramatic reduction in genetic diversity. We found one historical and eight recent mtDNA genotypes in 280 individuals that defined two highly divergent clades. In contrast to a previous, more limited, mtDNA analysis, sequences from these clades are not geographically restricted to eastern or southern African populations. Rather, we found a large admixture zone spanning populations from Botswana, Zimbabwe and south-eastern Tanzania. Mitochondrial and microsatellite differentiation between populations was significant and unique mtDNA genotypes and alleles characterized the populations. However, gene flow estimates (Nm) based on microsatellite data were generally greater than one migrant per generation. In contrast, gene flow estimates based on the mtDNA control region were lower than expected given differences in the mode of inheritance of mitochondrial and nuclear markers which suggests a male bias in long-distance dispersal.     

Remnant populations of the regal fritillary (Speyeria idalia) in Pennsylvania: Local genetic structure in a high gene flow species

The Regal Fritillary butterfly, Speyeria idalia (Drury) (Lepidoptera: Nymphalidae), has been described as a high gene flow species. Supporting this assertion, previous studies in the Great Plains, where it is still relatively widespread, have found evidence of gene flow across hundreds of kilometers. Using mitochondrial and microsatellite loci, we examined the spatial genetic structure of a very isolated Pennsylvania population of these butterflies that occupies three separate meadows located within ten kilometers of each other. We found restricted gene flow and a distinct structure, with each meadow having a unique genetic signature. Our findings indicate that even a species that normally exhibits high gene flow may show fine-scale genetic subdivision in areas where populations have been largely extirpated.Authors contributed equally.     

Effects of Pleistocene climatic and geomorphological changes on the population structure of the restricted-range catfish Trichogenes longipinnis (Siluriformes: Trichomycteridae)

Trichogenes longipinnis Britski & Ortega is a narrowly distributed endemic and phenotypically variable catfish from the coastal basins of the Serra do Mar range in southeast Brazil. We examined patterns of mtDNA variation of this species in coastal basins of the Serra do Mar to determine the influences of past climatic and geomorphological processes in connection with the currently isolated basins. Allozyme data were also used to test the hypothesis that the different spotting patterns in the different areas could be the result of cryptic speciation. Regardless of body pigmentation, T. longipinnis specimens from across the basins were found to belong to a single species, but the populations were structured in accordance with the current hydrological watersheds, in four management units across the three distinct basins of its geographic distribution. Thus, the current genetic distribution may be best explained by both marine regressions and orogeny. Based on the low levels of genetic variation and high population structure observed, we suggest that T. longipinnis should be classified as “vulnerable” in the Brazilian red list of threatened fauna. Furthermore, we propose that the headwaters of the Parati-Mirim River basin should be incorporated as an extension of the Bocaina National Park to protect its genetically differentiated lineages.     

Mitochondrial population structure and post‐glacial dispersal of longnose sucker Catostomus catostomus in Labrador,Canada: evidence for multiple refugial origins and limited ongoing gene flow

Two hundred and eighty‐seven longnose sucker Catostomus catostomus were collected from 14 lakes in Labrador, 52 from three lakes in Ontario, 43 from two lakes in British Columbia and 32 from a lake in Yukon; a total of 414 in all. The resulting 34 haplotypes (20 in Labrador) contained moderate haplotypic diversity (h = 0·657) and relatively low nucleotide diversity (π = 3·730 × 10^?3. Mean ?_ST (0·453, P < 0·05) over all populations revealed distinct genetic structuring among C. catostomus populations across Canada, based on province, which was validated by the analysis and spatial analysis of molecular variance (c. 80% variation between provinces). These results probably reflect the historical imprint of recolonization from different refugia and possibly indicate limited ongoing gene flow within provinces. A haplotype network revealed one major and two minor clades within Labrador that were assigned to the Atlantic, Beringian and Mississippian refugia, respectively, with tests of neutrality and mismatch distribution indicative of a recent population expansion in Labrador, dated between c. 3500 and 8300 years ago.     

Genetic diversity and gene flow within and between two different habitats of Primula merrilliana (Primulaceae), an endangered distylous forest herb in eastern China

Understanding whether and how different habitats shape population genetics is a fundamental question and a specific goal for evolutionary and conservation biology research. This study examined genetic diversity and gene flow within and between mountain and foothill habitats of Primula merrilliana, an endangered distylous forest herb in eastern China. Eleven population characteristics, including area, size and density variation, from the two habitats were also investigated. Mountain populations had significantly higher mean genetic diversity than foothill populations, which may be explained by stronger self‐incompatibility breeding system, more opportunity to use elevational shifts to track suitable sites under conditions of climate change and more heterogeneous environments in the former habitat, rather than by the differences of population size, gene flow and genetic drift intensity between them. Genetic analysis revealed that two distinct lineages, corresponding to the two habitats, diverged at China's ‘Last Glaciation’ (11 700–67 500 yr BP), suggesting this divergence was probably triggered by warmer climates during inter‐ (or post‐) glacial periods. Low unidirectional gene flow from mountain to foothill habitats, chiefly by seed dispersal, played a more important role in overall gene flow between habitats than within‐habitat gene flow. Within habitats, pollen contributes more substantially to gene flow than seed dispersal, especially in foothill habitats, possibly due to higher individual density and larger population sizes. These results have implications for the conservation in this and similar landscape areas and indicate the need to protect suitable habitats with wide elevational spans and sufficient size to permit ecological and elevational shifts in response to climatic changes. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 172–189.     

The role of waterholes as 'refugia' in sustaining genetic diversity and variation of two freshwater species in dryland river systems (Western Queensland, Australia)

1. Episodic floods and extended low or no flow periods characterise dryland river systems in Western Queensland, Australia. During protracted intervals between floods, rivers consist of a series of isolated waterholes, which serve as ‘refugia’ for aquatic species and much of the channel is dry. We categorised these waterholes into ‘main waterholes’, which are located in the main part of the river channel and ‘satellite waterholes’, which are located in distributary river channels. 2. We used mitochondrial sequences and allozymes to investigate levels of genetic diversity and patterns of connectivity among waterholes for two obligate freshwater species: Macrobrachium australiense (Decapoda: Palaemonidae) and Notopala sublineata (Gastropoda: Viviparidae). 3. We sampled 31 waterholes for M. australiense and 12 for N. sublineata. Based on a 505‐bp fragment of cytochrome oxidase subunit I, we identified 54 haplotypes in a sample of 232 individuals for M. australiense and based on a 457‐bp fragment of the same gene, 36 haplotypes in a sample of 145 individuals for N. sublineata. 4. Both nuclear and mitochondrial genetic data sets indicated that estimates of genetic diversity were not different in populations inhabiting main and satellite waterholes for either species. Also, there was generally very limited genetic differentiation among populations at any site. 5. We suggest that levels of connectivity among populations inhabiting waterholes at most sites are higher than expected. High levels of connectivity may help to maintain overall high levels of genetic diversity as well as low levels of genetic differentiation among waterholes within sites.     

Small-scale patterns of genetic variation in the mayfly Bungona narilla (Ephemeroptera: Baetidae) in rainforest streams, south-east Queensland

SUMMARY 1. Genetic structure of the mayfly Bungona narilla was examined using allozymes and a section of the cytochrome oxidase I gene.
2. The study had two major aims. The first was to determine whether patterns of genetic variation in mitochondrial DNA were similar to those found previously for allozymes, i.e. that more variation was evident among pools within a single stream than among streams. The mitochondrial DNA results were similar to those reported previously for allozymes, supporting the idea that larvae within any particular pool were unrepresentative of the total population and may result from a few matings.
3. The second aim was to test the hypothesis that the variation among pools within a stream was greater after dry periods than after wet periods. This was because after wet periods, larvae would have greater opportunity for mixing because of movement among pools. This hypothesis was partly supported by the mitochondrial DNA data but not by the allozyme data, in which variation among pools was extremely low on both sampling occasions. The reasons for this difference are unclear.     

Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani

Plethodon shermani comprises a series of geographically disjunct populations occupying high-elevation mountain isolates. These populations hybridize at their borders with salamanders of the Plethodon glutinosus species complex, and past range expansions inferred from Pleistocene climatic cycles may have increased the possible genetic interactions between P. shermani and species of the P. glutinosus complex. Because mitochondrial DNA haplotypes often show introgression across species borders, we survey mtDNA variation for evidence of past and ongoing genetic interactions between P. shermani, its close relative Plethodon cheoah, and species of the P. glutinosus complex. Ongoing hybridization with the P. glutinosus-complex species Plethodon teyahalee is accompanied by extensive mitochondrial introgression in some Unicoi populations of P. shermani, but it has little genetic impact on P. shermani populations outside hybrid zones at three other isolates (Tusquitee, Wayah Bald, Standing Indian). Some Unicoi populations of P. shermani exhibit mtDNA evidence of past hybridization with diverse lineages from P. aureolus and P. glutinosus. The Tusquitee isolate of P. shermani is also characterized by mtDNA haplotypes most closely related to Plethodon aureolus and P. glutinosus, presumably introduced by past genetic contact with these species or with introgressed populations of Unicoi P. shermani. The mtDNA variation in sampled populations of the Wayah Bald and Standing Indian isolates of P. shermani appears largely unaffected by ongoing hybridization. Principal components analyses of allozymic data indicate that P. shermani isolates collectively form a genetically homogeneous unit clearly demarcated from species with which they have had current or past genetic interactions. Rapid mtDNA introgression associated with transient contacts between P. shermani and other species permits a fine-level resolution of evolutionary lineages not evident from allozymic data.     

Biogeography and pattern of gene flow among Barbus species (Teleostei: Cyprinidae) inhabiting the Italian Peninsula and neighbouring Adriatic drainages as revealed by allozyme and mitochondrial sequence data

Genetic relationships among 24 Italian and Adriatic populations of barbs (genus Barbus ) were assessed using electrophoretic analysis of allozymes and mitochondrial DNA sequences of the cytochrome b gene. Results obtained with both markers were concordant, but they were not congruent with the current morphology-based systematics and taxonomy. Populations assigned to the same nominal taxa ( B. caninus , B. petenyi and B. rebeli ), were very divergent in both allozymes and mtDNA, indicating that these populations deserve recognition as different units for conservation and management. On the other hand, the two fluvio-lacustrine taxa considered as distinct species (i.e. B. plebejus and B. tyberinus ) are genetically very close to each other, showing no clear differences at either allozymes or mtDNA. The population of B. caninus from Pellice River carried allozyme alleles and mtDNA specific for B. plebejus , indicating a genetic introgression towards the former species. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 83–99.     

Genetic diversity and population structure of selected lacustrine and riverine populations of African catfish,Clarias gariepinus (Burchell, 1822), in Kenya

Determining the genetic characteristics of natural fish stocks is useful for conservation and aquaculture programs. For African catfish, Clarias gariepinus, genetic characterization could help identify populations suitable as brood stock for culture, and those in need of conservation. This study determined the genetic diversity, population structure, and demographic history of C. gariepinus from Lakes Victoria (LV), Kenyatta (LKE), Kamnarok (LKA), and Rivers Nyando (NR), Tana (TR) and Sosiani (SR) in Kenya. Using 128 DNA sequences of D-loop control region, 34 haplotypes were recovered, of which 79.4% were singletons. Only 7 haplotypes were shared between sites, implying little gene flow between sites. Number of haplotypes was highest in LKE and NR populations and lowest in SR. Haplotype diversity was highest in LV, and lowest in SR, while, nucleotide diversity was highest in LKA and lowest in LV. Phylogenetic analyses revealed five clusters: Lakes Victoria, Kamnarok and Kenyatta, and Rivers Tana and Nyando, from both maximum likelihood tree and minimum spanning network. This, together with significant F _ST values among the sites imply population differentiation. Mismatch distributions were multi-modal in LKA, LKE, NR and TR, signifying demographic equilibria. Neutrality tests Tajima`s D values for the sampled populations were negative and significantly different, suggesting stable populations. These results show the existence of genetically distinct populations of C. gariepinus that require spatially explicit management actions such as reducing fishing pressure, pollution, minimizing habitat destruction and fragmentation for sustainable utilisation of stocks.     

Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae)

We examined the consequences of barriers, stream architecture and putative dispersal capability on levels of genetic differentiation among populations of the freshwater fish Craterocephalus stercusmuscarum. Seven polymorphic allozyme loci and sequences of a 498-bp fragment of the ATPase 6 mitochondrial DNA (mtDNA) gene were used to assess patterns of genetic variation among 16 populations from upland and lowland streams of five drainages in northern Queensland, Australia. Concordant patterns at both genetic markers revealed that there were significant levels of genetic subdivision among all populations, while an analysis of molecular variation showed that the distribution of genetic diversity was not consistent with contemporary drainage structure. There were reciprocally monophyletic mtDNA clades and fixed or large frequency differences at allozyme loci either side of instream barriers such as waterfalls. This implied barriers were effective in restricting gene flow between upland and lowland populations separated by waterfalls. However, there were two genetically distinct groups in upland areas, even within the same subcatchment, as well as high levels of genetic subdivision among lowland populations, suggesting barriers alone do not explain the patterns of genetic diversity. The data revealed a complex phylogeographic pattern, which we interpreted to be the result of one or more invasion events of independent lineages to different sections of each drainage, possibly mediated by well documented geomorphological changes. Our results highlight the importance of earth structure and history in shaping population genetic structure in stream organisms where dispersal capability may be limited, and reveal that the contemporary structure of drainages is not necessarily a good indicator of genetic relationships among populations.     

Genetic and morphological variability of the European mudminnow Umbra krameri (Teleostei,Umbridae) in Serbia and in Bosnia and Herzegovina,a basis for future conservation activities

As a basis for future conservation activities, the genetic and external body morphology variability of the European mudminnow Umbra krameri, a highly endangered fish species in Serbia and in Bosnia and Herzegovina, was determined for existing populations with the use of molecular markers (mitochondrial and microsatellite DNA) and geometric morphometric methods. Mitochondrial DNA cytochrome b gene analysis revealed two previously undescribed haplotypes: Da1 (the Lugomir population from the Danube River basin) and Sa1 (the Bakreni Batar and the Gromi?elj populations from the Sava River system), with a corresponding genetic distance of 0·7%. Paired values of F_ST and D_AS distances for microsatellite marker data show that the difference between the Danube and the Sava populations is seven to nine times higher than the difference between the populations within the Sava River system. Geometric morphometric analyses also support a clear separation of the Lugomir population from the Bakreni Batar and the Gromi?elj populations. The analysis of the body shape variation, however, indicates a significant difference between the two genetically indistinguishable Sava populations. The observed genetic and phenetic relationships of the analysed mudminnow populations most probably represent a consequence of historical, geographical and ecological factors. These results will offer guidelines for future protection, conservation and sustainable management of this species in the region.     

Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long-lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the "model tree" genus Populus: Populus alba (white poplar) and Populus tremula (European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome-wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially from P. tremula to P. alba via P. tremula pollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal in P. tremula (pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity to P. alba seed parents, which maintains gene flow in the direction of P. alba despite smaller effective population sizes (N(e)) in this species (P. alba N(e)c. 500-550; P. tremula N(e)c. 550-700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergent Populus species.     

Patterns of population subdivision and gene flow in the ant Nothomyrmecia macrops reflected in microsatellite and mitochondrial DNA markers

The Australian endemic ant Nothomyrmecia macrops is renowned for having retained a large proportion of 'primitive' morphological and behavioural characters. Another less studied peculiarity of this species is the production of short-winged (brachypterous) female sexuals, which presumably are poor dispersers. The males, in contrast, bear a full set of normally developed wings and thus may disperse widely. We investigated patterns of genetic differentiation within and among three distantly separated populations in South Australia using nine polymorphic microsatellite loci and four regions of mitochondrial DNA (COI, COII, Cytb, lrRNA). We sampled eight subpopulations, one in the Lake Gilles CP, two near Penong and five around Poochera where distances ranged from 360 km to sites separated by 2-10 km. Only little differentiation was found at the local scale (within the assumed dispersal distance of males) using nuclear markers, whereas the three distant locations were moderately differentiated (FST = 0.06). Mitochondrial DNA genetic structure was much more pronounced on all scales (phiST = 0.98), with regular differences in both haplotype composition and frequency even occurring among closely located sites. This lack of congruence between nuclear and mitochondrial markers strongly suggests limited female dispersal and male-biased gene flow among populations. As to the conservation status of the species there is no evidence for severe population reductions in the recent past, which would have left populations genetically depauperate.     

When east meets west: population structure of a high-latitude resident species,the boreal chickadee (Poecile hudsonicus)

The population genetic structure of northern boreal species has been strongly influenced both by the Quaternary glaciations and the presence of contemporary barriers, such as mountain ranges and rivers. We used a combination of mitochondrial DNA (mtDNA), nuclear microsatellites and spatial distribution modelling to study the population genetic structure of the boreal chickadee (Poecile hudsonicus), a resident passerine, and to investigate whether historical or contemporary barriers have influenced this northern species. MtDNA data showed evidence of eastern and western groups, with secondary admixture occurring in central Canada. This suggests that the boreal chickadee probably persisted in multiple glacial refugia, one in Beringia and at least one in the east. Palaeo-distribution modelling identified suitable habitat in Beringia (Alaska), Atlantic Canada and the southern United States, and correspond to divergence dates of 60–96 kya. Pairwise F_ST values for both mtDNA and microsatellites were significant for all comparisons involving Newfoundland, though mtDNA data suggest a more recent separation. Furthermore, unlike mtDNA data, nuclear data support population connectivity among the continental populations, possibly due to male-biased dispersal. Although both are significant, the isolation-by-distance signal is much stronger for mtDNA (r²=0.51) than for microsatellites (r²=0.05), supporting the hypothesis of male-biased dispersal. The population structure of the boreal chickadee was influenced by isolation in multiple refugia and contemporary barriers. In addition to geographical distance, physical barriers such as the Strait of Belle Isle and northern mountains in Alaska are restricting gene flow, whereas the Rocky Mountains in the west are a porous barrier.     

Phylogeny and taxonomy of the genus Ilyodon Eigenmann, 1907 (Teleostei: Goodeidae), based on mitochondrial and nuclear DNA sequences

Taxonomy of the live‐bearing fish of the genus Ilyodon Eigenmann, 1907 (Goodeidae), in Mexico, is controversial, with morphology and mitochondrial genetic analyses in disagreement about the number of valid species. The present study accumulated a comprehensive DNA sequences dataset of 98 individuals of all Ilyodon species and mitochondrial and nuclear loci to reconstruct the evolutionary history of the genus. Phylogenetic inference produced five clades, one with two sub‐clades, and one clade including three recognized species. Genetic distances in mitochondrial genes (cytb: 0.5%–2.1%; coxI: 0.5%–1.1% and d‐loop: 2.3%–10.2%) were relatively high among main clades, while, as expected, nuclear genes showed low variation (0.0%–0.2%), with geographic concordance and few shared haplotypes among river basins. High genetic structure was observed among clades and within basins. Our genetic analyses, applying the priority principle, suggest the recognition only of Ilyodon whitei and Ilyodon furcidens, with I. cortesae relegated to an invalid species, the populations of which belong to I. whitei.     

Systematics of dusky salamanders, Desmognathus (Caudata: Plethodontidae), in the mountain and Piedmont regions of Virginia and North Carolina, USA

We analysed mitochondrial (cytochrome  b ) nucleotide sequences, nuclear allozyme markers, and morphometric characters to investigate species boundaries and phylogenetic relationships among dusky salamanders ( Desmognathus ) in the southern Blue Ridge and adjacent Piedmont Physiographic Provinces of Virginia and North Carolina. Our results revealed four distinct mitochondrial DNA clades that are also characterized by distinct allozyme markers. One clade consists of sequences derived from populations distributed from New England to south-western Virginia that are referable to Desmognathus fuscus Rafinesque, 1820, although there is considerable sequence and allozyme divergence within this clade. A second clade consists of sequences derived from populations referable to Desmognathus planiceps Newman, 1955, a form that we resurrect from its long synonymy under D. fuscus . Desmognathus planiceps and D. fuscus also differ in mandibular tooth shape. Two other cytochrome  b sequences recovered from populations along the Blue Ridge escarpment in southern Virginia are quite divergent from those of the previous two clades, and these populations may represent yet another distinct species. Sequences from a population in the Brushy Mountains in the Piedmont of northern North Carolina are similar to those of Desmognathus carolinensis . Population groupings indicated by allozyme data generally correspond to the cytochrome  b clades. Cryptic diversity in Appalachian desmognathan salamanders clearly requires further study. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 115–130.     

Patterns of gene flow and population genetic structure in the canyon treefrog, Hyla arenicolor (Cope)

Patterns of gene flow and genetic structuring were examined in the canyon treefrog, Hyla arenicolor (Cope). Hierarchical analysis of genetic variation was performed on mitochondrial cytochrome b haplotypes from 323 individuals, representing 32 populations from previously described phylogeographic regions. Results from AMOVA revealed that 60.4-78.9% of the recovered genetic variation was the result of differences in the appointment of genetic variation between subdivisions of the primary phylogeographic regions. In contrast, populations only contained between 13.9 and 30.1% of the observed haplotypic variation. Gene flow estimates based on calculations of phi ST revealed moderate levels of gene flow within phylogeographic regions, but there was no evidence of gene flow between these regions, suggesting that geographical boundaries were probably important in the formation of phylogeographic structure in H. arenicolor. Phylogeographic regions exhibited very different patterns of gene flow. One region showed evidence of recent colonization. Another region exhibited very limited gene flow. Moderate to high estimates of gene flow were obtained for populations from two distinct phylogeographic regions characterized by mesic and xeric environments. Isolation by distance was observed in both regions suggesting that these regions are in genetic equilibrium. Because gene flow is extremely unlikely between the populations in the xeric region, this result is interpreted as historical gene flow. These results indicate that isolation-by-distance effects may still be observed even when population genetic structure and gene flow are the result of historical association.     

Characterization of two cryptic species,Culicoides stigma and C.parroti (Diptera: Ceratopogonidae), based on barcode regions and morphology

Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are insect vectors of economically important veterinary diseases such as African horse sickness, bluetongue, and Schmallenberg virus. The identification of Culicoides based on morphological features can be difficult. Three species of biting midges, Culicoides nubeculosus, C. stigma, and C. parroti have emerged in the laboratory from mud collected around watering troughs on a farm in northern France. Emerging Culicoides were characterized morphologically and molecularly using molecular markers. The closely related species C. stigma and C.parroti showed highly divergent sequences for both mitochondrial (cytochrome B and cytochrome oxidase I) and ribosomal DNA first internal transcribed spacer. A RFLP based on a single restriction using the same enzyme (HaeIII) for both cytochrome C oxidase I and cytochrome B is proposed to identify these species.