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opencc-zeroDec 2014View details →

Data from: Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in South China and North Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China-Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China-Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3,900 years BP. The spatial differentiation of mtDNA and Y-chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock.

opencc-zeroDec 2018View details →

Data from: Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae

Aim: To quantify taxon diversity, biogeographic distributions and patterns of community assembly in xeniid octocorals using molecular operational taxonomic units (MOTUs). Location Red Sea, Indian and western Pacific Oceans. Taxon Xeniidae, a family of reef-dwelling octocorals (Anthozoa, Octocorallia). Methods Xeniids collected at 13 locations were sequenced at three barcode loci, and assigned to molecular operational taxonomic units (MOTUs) defined by minimum genetic distance thresholds. Taxon richness (no. of MOTUs) and endemicity (percent of MOTUs found at a single location) were quantified. Patterns of β-diversity (species turnover) and phylogenetic β-diversity (lineage turnover) among geographical regions were visualized using hierarchical clustering, NMDS plots, and distance-decay relationships. Community assembly was investigated by comparing the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) separating species in each assemblage to values generated for null communities. Results A genetic distance threshold of 0.3% discriminated 67 MOTUs, with taxon richness ranging from 2-18 MOTUs per site. Out of the 67 MOTUs, 48 (72%) were found at only a single location, and only two spanned both the western Indian and Pacific Oceans. Species turnover among sites was high, but phylogenetic β-diversity was lower than β-diversity and differed significantly from null models of community assembly at only two sites. β-diversity and phylogenetic β-diversity both increased significantly with geographic distance, and sites clustered into three distinct biogeographic regions (Red Sea and western Indian Ocean; Western Australia; western Pacific and Great Barrier Reef, Australia). All five major clades of xeniids were represented in each region. Main Conclusions A genetic approach to biodiversity estimation suggests that most xeniid taxa are regional endemics whose geographic distribution is likely governed by dispersal limitation. This conclusion contrasts with published records of certain morphospecies occurrences, which imply that they have broad geographic ranges. So far, the distribution of xeniid biodiversity mirrors that of scleractinian corals, with species richness highest in the Coral Triangle, but endemicity peaking in peripheral areas.

opencc-zeroDec 2012View details →

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.

opencc-zeroDec 2016View details →

Data from: Variation in the ecstatic display call of the Gentoo Penguin (Pygoscelis papua) across regional geographic scales

Geographic variation in bird vocalizations is common and has been associated with genetic differences and speciation, as well as with short-term changes in response to anthropogenic noise. Because vocalizations are used for individual recognition in many species, geographic variation in these traits may affect mate choice, pair bonding, and territory defense. Anecdotal evidence suggests the existence of geographic variation in vocalizations between isolated populations of Gentoo Penguins (Pygoscelis papua), but there have been no comprehensive studies of Gentoo Penguin vocalizations across a broad geographic range. We used acoustic recordings of ambient colony sound at 22 breeding colonies in the Antarctic Peninsula and South Shetland Islands, South Georgia, the Falkland Islands, and Argentina to address 2 main questions regarding Gentoo Penguin vocalizations: (1) How do ecstatic display calls vary both within and between individuals, colonies, and regions? (2) Can ecstatic display calls be used to distinguish subspecies? We found high levels of variation between individuals and between colonies, but little additional variation between regions or subspecies. We found no trends to suggest a latitudinal gradient in vocal characteristics, although we did find that some measures varied with relative distance between colonies. Although we found significant differences at the colony level, unknown calls could not easily be categorized to colony or region by machine learning. We conclude that the vocal soundscape of each colony is driven by variation between individuals within a colony and, developing independently from neighboring colonies, becomes differentiated from other colonies through a process of drift. Although individual calls could, in most cases, be identified to subspecies by machine learning, our analysis suggests that subspecies differences may be driven by variation among colonies and that subspecies identification may be unreliable using acoustics alone.

opennotspecifiedDec 2017View details →

FIGURES 3A–3E in Caddisflies (Insecta: Trichoptera) from Maranhão State, Northeast Region, Brazil: A new species, checklist, and new geographical records

FIGURES 3A–3E. Triplectides maranhensis sp. nov., male genitalia. 3A, abdominal segments IX and X, left lateral; 3B. terga IX and X and their preanal appendages (pr. ap.), dorsal; 3C, sternum IX, bearing inferior appendages, each with apicodorsal lobe (ap. lo.), basoventral lobe (bv. lo., right lobe omitted), and mesal lobe (me. lo.), ventral; 3D, phallic apparatus, left lateral; 3E, phallotremal sclerite, dorsal.

Fig. 1 in Geographic Distribution and Habitat Characterization of the Threatened Delta Green Ground Beetle, Elaphrus viridis Horn, 1878 (Coleoptera: Carabidae), in the Jepson Prairie Region of Solano County, California, USA

Fig. 1. Elaphrus viridis (DGGB). a) Green and bronze adult morph, b) Green adult morph, c) Third instar larva.

Fig. 4 in Geographic Distribution and Habitat Characterization of the Threatened Delta Green Ground Beetle, Elaphrus viridis Horn, 1878 (Coleoptera: Carabidae), in the Jepson Prairie Region of Solano County, California, USA

Fig. 4. Graph of sampling plots from the four habitat types and DGGB observations based on discriminant factors DF1 and DF2.

Fig. 3 in Geographic Distribution and Habitat Characterization of the Threatened Delta Green Ground Beetle, Elaphrus viridis Horn, 1878 (Coleoptera: Carabidae), in the Jepson Prairie Region of Solano County, California, USA

Fig. 3. Examples of habitat types sampled for DGGB (see text for additional information). a) Dense valley grassland (foreground), with bare ground as a trail, leading to a playa (background), b) Playa shoreline, illustrating both bare ground and densely vegetated shoreline areas, c) Vernal pool with dense valley grassland encroaching its shoreline, d) Scattered bare ground patches in dense valley grassland.

Fig. 2 in Geographic Distribution and Habitat Characterization of the Threatened Delta Green Ground Beetle, Elaphrus viridis Horn, 1878 (Coleoptera: Carabidae), in the Jepson Prairie Region of Solano County, California, USA

Fig. 2. Map of Jepson Prairie region, with locations of 81 playas color-coded by DGGB presence or absence.

opencc-zeroDec 2017View details →

Data from: Regional and local patterns of genetic variation and structure in yellow-necked mice − the roles of geographic distance, population abundance and winter severity

The goal of this study, conducted in seven large woodlands and three areas with small woodlots in north-eastern Poland in 2004-2008, was to infer genetic structure in yellow-necked mouse Apodemus flavicollis population and to evaluate the roles of environmental and population ecology variables in shaping the spatial pattern of genetic variation using 768 samples genotyped at 13 microsatellite loci. Genetic variation was very high in all studied regions. The primal genetic subdivision was observed between the northern and the southern parts of the study area, which harboured two major clusters and the intermediate area of highly admixed individuals. The probability of assignment of individual mice to the northern cluster increased significantly with lower temperatures of January and July and declined in regions with higher proportion of deciduous and mixed forests. Despite the detected structure, genetic differentiation among regions was very low. Fine-scale structure was shaped by the population density, whereas higher level structure was mainly shaped by geographic distance. Genetic similarity indices were highly influenced by mouse abundance (which positively correlated with the share of deciduous forests in the studied regions) and exhibited the greatest change between 0 and 1 km in the forests, 0 and 5 km in small woodlots. Isolation by distance pattern, calculated among regions, was highly significant but such relationship between genetic and geographic distance was much weaker, and held the linearity at very fine scale (~1.5 km), when analyses were conducted at individual level.

FIGURE 9 in Annotated checklist of Cerambycidae (Coleoptera: Chrysomeloidea) from the Brazilian semi-arid region, with new species and new geographic records

FIGURE 9. Distributional records of Cerambycidae from Brazilian semi-arid region. Legend of the brazilian states: MA = Maranh"o; CE = Ceará; PI = Piauí; RN = Rio Grande do Norte; PB = Paraíba; PE = Pernambuco; AL = Alagoas; SE = Sergipe; BA = Bahia; MG = Minas Gerais.

FIGURE 1. A–D in Annotated checklist of Cerambycidae (Coleoptera: Chrysomeloidea) from the Brazilian semi-arid region, with new species and new geographic records

FIGURE 1. A–D, Collection area in Fazenda Lagoa do Tamburi, Aracatu, Bahia, Brazil A, View of the vegetation around the weir located near the farmhouse; B, View of the dry forest area in the farm; C, Temporary stream in the dry forest area of the farm; D, Malaise trap in the dry forest area of the farm during the rainy season.

FIGURE 8. A–F in Annotated checklist of Cerambycidae (Coleoptera: Chrysomeloidea) from the Brazilian semi-arid region, with new species and new geographic records

FIGURE 8. A–F, Pseudomecas mourai sp. nov., holotype female: A–C, Dorsal, lateral, and ventral views; D, Head and pronotum, dorsal view; E, Head, ventral view; F, Head, frontal view; G, Labels.

FIGURE 5. A–F in Annotated checklist of Cerambycidae (Coleoptera: Chrysomeloidea) from the Brazilian semi-arid region, with new species and new geographic records

FIGURE 5. A–F, Species of Eburodacrys White, 1853, dorsal view: A, E. catarina Galileo & Martins, 1992, paratype, female (MZUSP); B, E. eburioides (White, 1853), male, Matelandia, Paraná, Brazil (MZUSP); C, E. flexuosa Gounelle, 1909, male, Buena Vista, Santa Cruz, Bolivia (MZUSP); D, E. lancinata Napp & Martins, 1980, holotype, female (MZUSP); E, E. lenkoi Napp & Martins, 1980, holotype, male (MZUSP); F, E. tuberosa Gounelle, 1909, syntype, female, Goiás, Brazil (MZUSP).

FIGURE 6. A–D in Annotated checklist of Cerambycidae (Coleoptera: Chrysomeloidea) from the Brazilian semi-arid region, with new species and new geographic records

FIGURE 6. A–D, Coccoderus costae sp. nov. Holotype female: A–C, Dorsal, lateral, and ventral views; D, Head and prothorax (dorsal view); E, Labels. F, Coccoderus sexmaculatus Buquet, 1840, female, dorsal view, Itatiaia, Rio de Janeiro, Brazil (MZUSP).

FIGURE 4. A–F in Annotated checklist of Cerambycidae (Coleoptera: Chrysomeloidea) from the Brazilian semi-arid region, with new species and new geographic records

FIGURE 4. A–F, Eburodacrys boteroi sp. nov., holotype female: A–C, Dorsal, lateral, and ventral views; D, Head and prothorax (dorsal view); E, Head (frontal view); F, Mesofemur and metafemur, laterofrontal view; G, Labels. Legend: tb = tubercles; ls = lateral spine