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161 results for “geographic structure”
Data from: Contrasting effects of landscape features on genetic structure in different geographical regions in the ornate dragon lizard, Ctenophorus ornatus
Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend that fine-scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (FST = 0.12), as well as isolation-by-distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal-lag in the response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure.
Data from: Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure
Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the "shallow" and "deep" groups, beyond the Irminger Sea where they were described previously. A third group, "slope," has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression.
Data from: Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow
The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In western Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviours. To investigate patterns of macro-geographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west, central and southern African genetic clusters. These clusters are coincident with the central African rainforest belt and northern and southern savannah biomes, which suggests restrictions to gene flow associated with the transition between these biomes. By contrast geographically patterned population substructure appears much weaker within the S-form.
Data from: Contrasting patterns of clonality and fine-scale genetic structure in two rare sedges with differing geographic distributions
For plants with mixed reproductive capabilities, asexual reproduction is more frequent in rare species and is considered a strategy for persistence when sexual recruitment is limited. We investigate whether asexual reproduction contributes to the persistence of two co-occurring, rare sedges that both experience irregular seed set and if their differing geographic distributions have a role in the relative contribution of clonality. Genotypic richness was high (R=0.889±0.02) across the clustered populations of Lepidosperma sp. Mt Caudan and, where detected, clonal patches were small, both in ramet numbers (less than or equal to3 ramets/genet) and physical size (1.3±0.1 m). In contrast, genotypic richness was lower in the isolated L. sp. Parker Range populations, albeit more variable (R=0.437±0.13), with genets as large as 17 ramets and up to 5.8 m in size. Aggregated clonal growth generated significant fine-scale genetic structure in both species but to a greater spatial extent and with additional genet-level structure in L. sp. Parker Range that is likely due to restricted seed dispersal. Despite both species being rare, asexual reproduction clearly has a more important role in the persistence of L. sp. Parker Range than L. sp. Mt Caudan. This is consistent with our prediction that limitations to sexual reproduction, via geographic isolation to effective gene exchange, can lead to greater contributions of asexual reproduction. These results demonstrate the role of population isolation in affecting the balance of alternate reproductive modes and the contextual nature of asexual reproduction in rare species.
Data from: Novel concordance between geographic, environmental and genetic structure in the ecological generalist prickly sculpin (Cottus asper) in California
Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California. We then incorporated genetic and GIS data into ecological niche models to assess ecological conditions within identified groups. Though not reciprocally monophyletic, unique mtDNA haplotypes, microsatellite clustering, and measures of isolation by distance (Coastal: r = 0.960, P < 0.001; Inland: r = 0.277, P = 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained to Great Central Valley). Divergence estimates of 41–191 kya combined with the regional biogeographic history suggest geographic barriers are absent between groups since divergence, but ecological niche modeling revealed significant environmental differences (t = 10.84, P < 0.001). Introgressed individuals were also discovered between groups in an ecologically and geographically intermediate region. Population structure was limited, predominately found in tributaries of the San Joaquin basin in the Inland group. Overall, C. asper exhibited substantial genetic diversity, despite its ecological generality, reflecting California's historically unique and complex hydrology. More broadly, this study illustrates variable environments within the range of a generalist species may mask genetic divergences and should not be overlooked in biodiversity assessments.
Data from: Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single nucleotide polymorphism data
Marine systems have traditionally been thought of as "open" with few barriers to gene flow. In particular, many marine organisms in the Southern Ocean purportedly possess circumpolar distributions that have rarely been well verified. Here, we use the highly abundant and endemic Southern Ocean brittle star Ophionotus victoriae to examine genetic structure and determine whether barriers to gene flow have existed around the Antarctic continent. Ophionotus victoriae possesses feeding planktotrophic larvae with presumed high dispersal capability, but a previous study revealed genetic structure along the Antarctic Peninsula. To test the extent of genetic differentiation within O. victoriae, we sampled from the Ross Sea through the eastern Weddell Sea. Whereas two mitochondrial DNA markers (16S rDNA and COI) were employed to allow comparison to earlier work, a 2b-RAD single-nucleotide polymorphism (SNP) approach allowed sampling of loci across the genome. Mitochondrial data from 414 individuals suggested three major lineages, but 2b-RAD data generated 1,999 biallelic loci that identified four geographically distinct groups from 89 samples. Given the greater resolution by SNP data, O. victoriae can be divided into geographically distinct populations likely representing multiple species. Specific historical scenarios that explain current population structure were examined with approximate Bayesian computation (ABC) analyses. Although the Bransfield Strait region shows high diversity possibly due to mixing, our results suggest that within the recent past, dispersal processes due to strong currents such as the Antarctic Circumpolar Current have not overcome genetic subdivision presumably due to historical isolation, questioning the idea of large open circumpolar populations in the Southern Ocean.
Data from: Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents
Background: Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each generation via infection by free-living forms. This study examined geographical subdivision of the thiotrophic endosymbionts hosted by Bathymodiolus mussels living along the eastern Pacific hydrothermal vents. High-throughput sequencing data of 16S ribosomal RNA encoding gene and fragments of six protein-coding genes of symbionts were examined in the samples collected from nine vent localities at the East Pacific Rise, Galápagos Rift, and Pacific-Antarctic Ridge. Results: Both of the parapatric sister-species, B. thermophilus and B. antarcticus, hosted the same numerically dominant phylotype of thiotrophic Gammaproteobacteria. However, sequences from six protein-coding genes revealed highly divergent symbiont lineages living north and south of the Easter Microplate and hosted by these two Bathymodiolus mussel species. High heterogeneity of symbiont haplotypes among host individuals sampled from the same location suggested that stochasticity associated with initial infections was amplified as symbionts proliferated within the host individuals. The mussel species presently contact one another and hybridize along the Easter Microplate, but the northern and southern symbionts appear to be completely isolated. Vicariance associated with orogeny of the Easter Microplate region, 2.5–5.3 million years ago, may have initiated isolation of the symbiont and host populations. Estimates of synonymous substitution rates for the protein-coding bacterial genes examined in this study were 0.77–1.62%/nucleotide/million years. Conclusions: Our present study reports the most comprehensive population genetic analyses of the chemosynthetic endosymbiotic bacteria based on high-throughput genetic data and extensive geographical sampling to date, and demonstrates the role of the geographical features, the Easter Microplate and geographical distance, in the intraspecific divergence of this bacterial species along the mid-ocean ridge axes in the eastern Pacific. Altogether, our results provide insights into extrinsic and intrinsic factors affecting the dispersal and evolution of chemosynthetic symbiotic partners in the hydrothermal vents along the eastern Pacific Ocean.
Data from: The geographic structure of selection on a coevolving interaction between social parasitic wasps and their hosts hampers social evolution
Social parasites exploit societies, rather than organisms, and rear their brood in social insect colonies at the expense of their hosts, triggering a coevolutionary process that may affect host social structure. The resulting coevolutionary trajectories may be further altered by selection imposed by predators, which exploit the abundant resources concentrated in these nests. Here, we show that geographic differences in selection imposed by predators affects the structure of selection on coevolving hosts and their social parasites. In a multi-year study, we monitored the fate of the annual breeding attempts of the solitary-founding females of Polistes biglumis social wasps in four geographically distinct populations that varied in levels of attack by the congeneric social parasite, P. atrimandibularis. Foundress fitness depended mostly on whether, during the long founding phase, a colony was invaded by social parasites or attacked by predators. Foundresses from each population differed in morphological traits and reproductive tactics that were consistent with selection imposed by their natural enemies and in ways that may affect host sociality. In turn, parasite traits were consistent with selection imposed locally by hosts, implying a geographic mosaic of coevolution in this brood parasitic interaction.
Data from: Plant geographic origin and phylogeny as potential drivers of community structure in root-inhabiting fungi
1. Root-inhabiting fungal communities, including mutualists and antagonists, influence host plant performance, and can potentially shape plant community composition. However, there is uncertainty about how root-inhabiting fungal communities are structured, and if fungal community characteristics are significant predictors of host plant abundance. 2. In this study, we first assessed how root-inhabiting fungal communities were structured in relation to the phylogeny and geographic origins (native vs exotic) of their host plants in an old-field community. In addition, we took into consideration the spatial arrangements (i.e. physical locations) of the individual host plants. We then tested if the relative abundances of pathogenic and beneficial arbuscular mycorrhizal (AM) fungi could predict host plant abundances. 3. We found that host plant phylogeny was an important factor in structuring the whole fungal community, irrespective of host plant origin. Furthermore, the spatial arrangements of individual host plants were a strong predictor of AM fungal community structure. Host plant phylogeny and spatial arrangements appeared to similarly affect the structure of pathogenic fungal communities. No distinct differences were observed between native and exotic plant species in fungal community characteristics. The relative abundances of AM and pathogenic fungi were not significant predictors for observed abundances of their host plants. 4. Synthesis. Host plant phylogeny and spatial arrangements can structure naturally occurring root-inhabiting fungal communities. The absence of distinct differences in fungal community composition, including pathogens, in exotic and native plants suggests long residence times and the consequent naturalization of exotic species in the region, allowing for the establishment of similar plant-microbial interactions between native and exotic species.
FIGURE 6 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 6. Selected cranial traits in adult (except noted) Juliomys pictipes (CIES-M 23). A. Rostrum in dorsal view: note the inconspicuous zygomatic notches and broad zygomatic root; B. Interorbital region: the arrow indicates incomplete fusion in the anterior part of the interfrontal suture; C. Interorbital region in a juvenile specimen (CNP 895); D. Rostrum in lateral view: note the almost absence of upper free border in the zygomatic plate; E. Interfrontal depression; F. Mesopterygoid fossa; G. Palatal and postpalatal region of a juvenile specimen (CNP 895): note the complete ossification of the mesopterygoid fossa roof; H. Temporal region; I. Braincase; J. Auditory capsule: note the extension of the meatus; K. Squamosal-alisphenoid region; L. Upper first molar detail: note the crested corona and the well developed mesoloph. Abbreviations: acl = anterior opening alisphenoid canal, bu = auditory capsule, cc = carotid canal, d = interfrontal depression, f = frontal, fo = foramen ovale, i = interparietal, m = maseteric tubercle, M1 = first upper molar, M2 = second upper molar, M3 = third upper molar, ma = meatus, mb = trough for masticatory-buccinator nerve, mf = mesopterygoid fossa, ms mesoloph, mt = mastoid, mx = maxilla, na = nasal, oc = occipital, p = lateral portion of the parietal, pa = parapterygoid fossa, pm = premaxilla, ppp = postpalatal posterolateral pit, pr = parietal, r = zygomatic root, sb = supernumerary bone, sq = squamosal, t = tegmen tympani, zp = zygomatic plate.
FIGURE 5 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 5. Lateral, dorsal and ventral views of the skull of Juliomys pictipes (CIES-M 23) from Misiones, Argentina (scale = 5 mm).
FIGURE 8 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 8. Stomach of Juliomys pictipes (CNP 895): internal view of the dorsal half. Abbreviations: p: pilorous; ia: incisura angularis; e: esophagus; ce: cornified squamous epithelium; co: corpus; bf: bordering fold; ge: glandular epithelium; a: antrum.
FIGURE 4 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 4. Manus and pes of Juliomys pictipes from Misiones, Argentina (MLP 1.I.03.24): a. Manus, palmar surface; b. Pes, dorsal surface (note the bicolor condition); c. Pes, plantar surface.
FIGURE 2 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 2. Recording localities of Juliomys pictipes: ARGENTINA: MISIONES: 1. Parque Nacional Iguazú; 2. Parque Provincial "Ernesto Che Guevara;" 3. Reserva Privada de Usos Múltiples de la Universidad Nacional de La Plata "Valle del Arroyo Cuña Pirú"; BRAZIL: SÃO PAULO: 4. Buri; not specific locality provided; 5. Mulheres and Museros; 6. Fazenda Sakamoto, Campinho; Fazenda Sakamoto, Portão; Fazenda Intervales; 7. Fragmento Citadini; Fragmento Divisa; Três Quedas; Moacir; Paraguai; Cogumelo; 8. Floresta Nacional de Ipanema, 20 km NW Sorocaba; 9. Piedade, not specific locality provided; 10. Reserva Florestal do Morro Grande, Caucaia do Alto; 11. Riacho Grande; 12. Parque Natural Municipal da Serra do Itapety; RIO DE JANEIRO: 13. Mata do Mamede; 14. Fazenda Boa Fė; MINAS GERAIS: 15. Reserva Particular do Patrimȏnio Natural do Caraça, 25 km SW Santa Barbara; 16. Estação de Pesquisa e Desenvolvimento Ambiental de Peti. The grey area represents the approximate cover of the Atlantic Forest.
FIGURE 3 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 3. External aspect (lateral view) of a recently collected Juliomys pictipes from Misiones, Argentina (MLP 1.I.03.24).
FIGURE 7 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 7. Selected mandible traits in adult Juliomys pictipes (CIES-M 23). A. Anterior region of the horizontal ramus: note the depressed position of the diastema anterior point with respect to the alveolar plane; B. Ascending ramus region: note the short angular process. Abbreviations: cp = capsular projection, m1 = first lower molar, m2 = second lower molar, m3 = third lower molar, me = mental foramen, ml = maseteric crest, lower ridge, mu = maseteric crest, upper ridge.
FIGURE 1 in Rediscovery of Juliomys pictipes (Rodentia: Cricetidae) in Argentina: emended diagnosis, geographic distribution, and insights on genetic structure
FIGURE 1. Strict consensus tree of the 300 most parsimonious trees (length 1048 steps, CI = 0.483, RI = 0.606) obtained in the maximum parsimony analysis of the cytochrome b gene sequences. Numbers above branches indicate parsimony jackknife (left), Bremer support (middle), and maximum likelihood bootstrap (right) values of the nodes to their right. Only jackknife and bootstrap values> 50 % are shown. * indicates that the node in question was not recovered in the maximum likelihood analyses; in that analysis J. rimofrons and J. pictipes are sister to each other but with less than 50 % of support.
Geographic drivers more important than landscape composition in predicting bee beta diversity and community structure
<p>The importance of microhabitat traits such as floral availability is well known; however, forest bee spatial dynamics have been variably studied across local to broad geographic scales. Past literature suggests that landscape factors from proximate to distal are important in determining forest bee community metrics, including richness, abundance, and taxonomic composition. Leveraging the interest and assistance of citizen science volunteers, we employed standard bee bowl trap transects across Maryland, Delaware, northern Virginia, and the District of Columbia and identified correlations between bee community composition, local and regional landcover, and broader geospatial patterns. We also identified the partial contributions of both specific species and sampling sites to total beta diversity. Various landcover metrics were significantly related to bee community structure, with bee abundance positively and negatively correlated with forest and wetland cover, respectively. In general, land cover metrics within a 1,000-m buffer exhibited stronger correlations with bee communities; however, broader geographic variation, using Cartesian coordinates north and east as indices, was most significantly correlated with the bee community. Specifically, bee communities were less rich to the east and south of the study area. We also identified similar correlations with the bee community as categorized both by trophic and nesting behaviors, with both geographic northing and easting proving to be most strongly correlated with the forest bee community. Results of beta diversity and cluster analyses showed that the most species-depauperate sites exhibited the highest contributions to beta diversity and that species-poor sites consisted of a reduced subset of the greater community. Our results show that successful bee conservation must consider, beyond local-scale resource availability, broad geospatial considerations and forest habitat connectivity across political and administrative boundaries.</p>
Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure
<p class="MsoNoSpacing">Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus <i>Ommatotriton</i>) from the Near East has been proposed to contain three species (<i>O. nesterovi</i>, <i>O. ophryticus </i>and <i>O. vittatus</i>) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between <i>O. nesterovi</i> and <i>O. ophryticus</i> is suggested. We find evidence for introgression between <i>O. nesterovi</i> and <i>O. ophryticus</i>, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, <i>O. vittatus cilicensis</i>, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.</p>
Supplementary material 2 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 5: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae and Bactrocera dorsalis populations. The highest Betweenness-centrality is highlighted in blue.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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OpenNeuro
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