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FIGURE 8. Branch containing Desmognathus quadramaculatus, D. marmoratus and D in Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

FIGURE 8. Branch containing Desmognathus quadramaculatus, D. marmoratus and D. folkertsi pruned from Bayesian majority-rule consensus phylogram, diamonds represent posterior probabilities> 0.90. Numbers following species names in parenthesis represent population sample numbers.

FIGURE 7. Sampling localities for Desmognathus imitator and D in Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

FIGURE 7. Sampling localities for Desmognathus imitator and D. aeneus, symbols match those in Fig. 5B and 5C respectively.

FIGURE 4 in Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

FIGURE 4. Maximum-likelihood reconstruction, numbers above branches represent bootstrap support values (only bootstrap values below 100% are shown), clades are labeled as in Figure 3.

FIGURE 2 in Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades

FIGURE 2. Color-coded profile of the Level IV Ecoregions present in the Pee Dee and Santee River drainages; the number of dusky salamander species present in each level IV ecoregion X drainage sample unit (based on current distribution maps) is shown.

opennotspecifiedAug 2019View details →

FIGURES 7–12 in Aphonopelma braunshausenii Tesmoingt, 1996 is a nomen dubium, with review of some historic morphological characters ineffective at species delineation (Araneae: Theraphosidae)

FIGURES 7–12. Labia of the above Aphonopelma specimens all showing near identical morphology in shape and cuspule density, 7 Aphonopelma platnicki holotype male BMNH 1894.2.18.1, 8 Aphonopelma clarki holotype female BMNH 1959.1.2 [= A. hentzi Girard, 1853 per Hamilton et al. 2016)], 9 Aphonopelma anax non-type male OUMNH 2009-001, 10 Aphonopelma pallidum holotype male BMNH 1898.12.24.34–37, 11 Aphonopelma bicoloratum non-type male OUMNH 2011-045, 12 Aphonopelma marxi non-type male OUMNH 2007-064. Scale lines = 1mm.

opennotspecifiedAug 2019View details →

FIGURES 1–6 in Aphonopelma braunshausenii Tesmoingt, 1996 is a nomen dubium, with review of some historic morphological characters ineffective at species delineation (Araneae: Theraphosidae)

FIGURES 1–6. Ocular tubercles of some Aphonopelma species showing variation in size and distance between eyes, 1 Aphonopelma platnicki holotype male BMNH 1894.2.18.1, 2 Aphonopelma clarki holotype female BMNH 1959.1.2 [= A. hentzi Girard, 1853 per Hamilton et al. 2016)], 3 Aphonopelma anax non-type male OUMNH 2009-001, 4 Aphonopelma pallidum holotype male BMNH 1898.12.24.34–37, 5 Aphonopelma bicoloratum non-type male OUMNH 2011-045, 6 Aphonopelma marxi nontype male OUMNH 2007-064. Scale lines = 1mm.

opencc-zeroSep 2021View details →

Biogeographic divides in East Asia delineated by the three-step landforms of China and the East China Sea: insights from phylogeographical breaks of Kerria japonica

Aim: East Asia exhibits complex geomorphological and climatic characteristics. The aim of this study is to test whether the biogeographic divides present along the so-called three-step landforms of China and the East China Sea (ECS), and provide insight into the evolution the East Asian Flora (EAF) with respect to Hengduan Mountains, Central China and East China. Location: East Asia Taxon: Kerria japonica, a deciduous shrub distributed in subtropical mixed evergreen and deciduous broadleaved forests of East Asia. Methods: Three chloroplast DNA (cpDNA) regions and 15 nuclear microsatellite (nSSR) loci were sequenced/genotyped in 576/450 individuals. We performed phylogeographical analyses to assess genetic structure, historical gene flow and demographic history. Climate factors were examined to identify their effects on the phylogeographical breaks. Time-calibrated phylogenetic trees and ancestral range reconstruction were used to infer biogeographic history. Potential habitats at present and in the past (LIG, LGM) were identified using ecological niche modelling (ENM). Results: Distinct phylogeographical breaks were found along the ECS and the edges of the three-step landforms of China. Low historical gene flow and significant climatic differences were detected in each pair of adjacent regions. Compared with the quite stable distribution range on the Chinese mainland, Japanese populations had experienced obvious northward expansion after the LGM in response to Quaternary climate change. Main conclusions: K. japonica has a complex biogeographic history, with a Mid-Miocene origin in North America and subsequent migration into East Asia via the Bering land bridge. The onset of intra-specific diversification was probably associated with the Asian monsoon intensifications, while the CJK land bridge facilitated the formation of the Japan lineage (6.78 Ma). The spatiotemporal population differentiation in Chinese mainland demonstrates the significant role of biogeographic divides delineated by three-step landforms of China; and provides clues to help understand the floristic regionalization and evolutionary history of plant diversity in East Asia, especially with respect to the Hengduan Mountains, Central China and East China.

opencc-zeroDec 2017View details →

Data from: Partitioning drivers of spatial genetic variation for a continuously-distributed population of boreal caribou: implications for management unit delineation

Isolation-by-distance (IBD) is a natural pattern not readily incorporated into theoretical models nor traditional metrics for differentiating populations, although clinal genetic differentiation can be characteristic of many wildlife species. Landscape features can also drive population structure additive to baseline IBD resulting in differentiation through isolation-by-resistance (IBR). We assessed the population genetic structure of boreal caribou across western Canada using non-spatial (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the relative contribution of IBD and IBR on genetic variation of 1221 boreal caribou multilocus genotypes across western Canada. We further introduced a novel approach to compare the partitioning of individuals into management units (MU) and assessed levels of genetic connectivity under different MU scenarios. STRUCTURE delineated five genetic clusters while MEMGENE identified finer-scale differentiation across the study area. IBD was significant and did not differ for males and females both across and among detected genetic clusters. MEMGENE landscape analysis further quantified the proportion of genetic variation contributed by IBD and IBR patterns, allowing for the relative importance of spatial drivers, including roads, water bodies and wildfires, to be assessed and incorporated into the characterization of population structure for the delineation of MUs. Local population units, as currently delineated in the boreal caribou recovery strategy, do not capture the genetic variation and connectivity of the ecotype across the study area. Here, we provide the tools to assess fine-scale spatial patterns of genetic variation, partition drivers of genetic variation and evaluate the best management options for maintaining genetic connectivity. Our approach is highly relevant to vagile wildlife species that are of management and conservation concern and demonstrate varying degrees of IBD and IBR with clinal spatial genetic structure that challenges the delineation of discrete population boundaries.

opencc-zeroDec 2015View details →

Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

The honeybee (Apis mellifera) has been threatened by multiple factors, including pests and pathogens, pesticides, and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A.m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify purebred A.m. mellifera colonies. Microsatellites have been preferred for identification of A.m. mellifera stocks across conservation centers. However, owing to high-throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite dataset to detect structure and introgression with that of different datasets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellites. Contrary to every SNP dataset, microsatellites were unable to clearly separate the two European lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level microsatellites' performance was relatively poor at the upper range of introgression, a result reflected by their lower precision. Although mean accuracy was relatively high across datasets (>91%), microsatellites were the least accurate and the top-ranked informative 144 SNPs were the most accurate. Comparisons amongst the SNP datasets showed that those combining SNPs flanking microsatellites performed worst. Our results suggest that SNPs are more powerful for identification of A.m. mellifera colonies, especially when they are selected by information content.

opencc-zeroDec 2014View details →

Data from: The importance of delineating networks by activity type in bottlenose dolphins (Tursiops truncatus) in Cedar Key, Florida

Network analysis has proved to be a valuable tool for studying the behavioural patterns of complex social animals. Often such studies either do not distinguish between different behavioural states of the organisms or simply focus attention on a single behavioural state to the exclusion of all others. In either of these approaches it is impossible to ascertain how the behavioural patterns of individuals depend on the type of activity they are engaged in. Here we report on a network-based analysis of the behavioural associations in a population of bottlenose dolphins (Tursiops truncatus) in Cedar Key, Florida. We consider three distinct behavioural states—socializing, travelling and foraging—and analyse the association networks corresponding to each activity. Moreover, in constructing the different activity networks we do not simply record a spatial association between two individuals as being either present or absent, but rather quantify the degree of any association, thus allowing us to construct weighted networks describing each activity. The results of these weighted activity networks indicate that networks can reveal detailed patterns of bottlenose dolphins at the population level; dolphins socialize in large groups with preferential associations; travel in small groups with preferential associates; and spread out to forage in very small, weakly connected groups. There is some overlap in the socialize and travel networks but little overlap between the forage and other networks. This indicates that the social bonds maintained in other activities are less important as they forage on dispersed, solitary prey. The overall network, not sorted by activity, does not accurately represent any of these patterns.

opencc-zeroDec 2016View details →

Data from: Revisiting the provenance delineation of a widespread shrub, Frangula alnus—the role of spatial, temporal and environmental patterns

Including population genetic aspects into the selection of planting material within the framework of conservation and restoration measures is of vital importance for the long-term persistence of populations. This is especially true facing climate change since genetic diversity and the spread of potentially beneficial alleles are important for the adaptability of populations. Therefore, knowledge about genetic variability within and between populations is a critical aspect when determining provenance regions. In our study, we investigated the population genetic structure of a widespread, insect-pollinated and mainly bird-dispersed shrub species, Frangula alnus, on the basis of seven microsatellites and two chloroplast DNA markers throughout Germany. The aim was to determine the spatial, temporal and ecological processes genetically structuring populations to critically revise existing provenance regions. Therefore, we conducted analyses on different spatial scales (country-wide, regional and local) using the two different marker sets in addition to environmental variables. We detected distinct patterns on all spatial scales which indicated influences of historic recolonization processes, regional differences of seed dispersal across the landscape, as well as small-scale spatial genetic structures attributable to local dispersal processes. No relation of underlying environmental gradients such as temperature or precipitation and genetic patterns was found. We conclude that different aspects of historic and more recent gene flow shape population genetic structures and that a thorough analysis on a variety of spatial, temporal and environmental scales is necessary to appropriately select planting material for conservation and restoration measures. Correspondingly, management advice regarding provenance delineations will be provided.

opencc-zeroDec 2014View details →

Data from: The Parmotrema acid test: a look at species delineation in the P. perforatum group 40 y later

Parmotrema perforatum and its relatives form a morphologically distinctive group of species, most of which are common and endemic to eastern North America. Species delimitation in this ecologically important group was the subject of extensive inquiry before the advent of molecular systematics and computationally intensive niche modeling. As part of a large-scale lichen biodiversity inventory of the Mid-Atlantic Coastal Plain, we used ITS sequence data to examine the utility of characters (morphological, chemical, reproductive, ecological) in circumscribing four species in this group (P. hypoleucinum, P. hypotropum, P. perforatum, P. subrigidum). We found that P. hypoleucinum and P. subrigidum as currently circumscribed are monophyletic and the latter comprises two chemotypes differing in the presence or absence of norstictic acid in addition to alectoronic acid. The sequences of P. hypotropum and P. perforatum, which are chemically identical species and differ only in reproductive mode, were intermixed in a single, well-supported clade. The two chemotypes of P. subrigidum are partially allopatric and their sequences are > 99% identical. Nonetheless, niche modeling suggests they occupy significantly different ecological niches. These results provide a new perspective on much-debated questions on species circumscription in lichens and suggest new avenues for genetic, ecological and systematic research.

opencc-zeroDec 2013View details →

Data from: Morphological vs. molecular delineation of taxa across montane regions in Europe: the case study of Gammarus balcanicus Schäferna, 1922 (Crustacea: Amphipoda)

Mountainous areas are characterized by substantial biodiversity and endemicity due to their complex geological history and habitat fragmentation. Hence, it can be assumed that particularly high species richness can be found in organisms with limited dispersal capabilities that inhabit mountain streams. A number of scientific papers focus on molecular phylogeography or traditional taxonomy of species or species groups inhabiting such habitats. However, there is a lack of studies that integrate morphological and molecular data to identify and delineate cryptic species. For practical reasons, uncovering cryptic diversity is crucial in taxa used in biomonitoring. Distinct species, hard to separate based on morphology only, may have different tolerance ranges towards a variety of factors. Thus, our goal is to combine the two approaches to reveal potential patterns of diversification within a species widely distributed across European mountains: the amphipod crustacean Gammarus balcanicus. The data were obtained from 13 populations spread across the range of the species. Individuals were initially ascribed to G. balcanicus based on conventional fauna key morpho-anatomical diagnostic features and were further analysed for 23 additional features to explore any putative diversification. Morphometric data were analysed with use of the multiple correspondence analysis and anova. Molecular distances were calculated for 551-bp-long COI sequences. Test for isolation by distance was performed for both morphological and molecular data. The morphometric studies showed that some of the analysed features differed significantly between populations, although there was only a weak correlation between the morphological divergence and the between-population geographical distances. Moreover, high morphological diversity was present within sites. A set of 42 COI haplotypes was identified among the 135 individuals sequenced. No haplotype was shared among populations. The molecular p-distances within the nine localities presenting more than one haplotype were either almost null (ca. <0.003 for 7 localities) or relatively low (ca. 0.01–0.02 for 2 localities). In opposite, the molecular p-distances between localities were mostly at a high level (94% of pairwise comparisons being >0.14), similar as between other well-defined species of the genus Gammarus. Surprisingly, G. balcanicus appears to be polyphyletic based on topology of the neighbour-joining tree. The level of genetic distance between localities was not correlated with their geographical proximity. Globally, combining spatial patterns of morphological versus molecular divergence indicates a high level of cryptic diversity within a species conventionally defined based upon fauna key morphological features. In this context, the name G. balcanicus should be applied only to the population from locus typicus, while the other populations represent a number of putative distinct species. We may expect that such phenomenon would apply also to other animal taxa with conserved morphology, which are widespread over different mountain ranges in Europe.

FIGURE 10. P in New species and records of Pyrgulopsis (Gastropoda: Hydrobiidae) from the Snake River basin, southeastern Oregon: further delineation of a highly imperiled fauna

FIGURE 10. P. intermedia (Tryon). A–D. Shells. Scale = 1.0 mm. A. JFBM 20507. B. USNM 1107071. C. USNM 1107076. D. USNM 1075362.

FIGURE 2 in New species and records of Pyrgulopsis (Gastropoda: Hydrobiidae) from the Snake River basin, southeastern Oregon: further delineation of a highly imperiled fauna

FIGURE 2. Maximum parsimony (MP) tree based on the COI dataset (TL = 322, CI = 0.64). Bootstrap support for nodes is provided when>70%. Bold-faced sequences are newly reported herein. Scale bar = one substitutional change per 100 nucleotide positions.

FIGURE 4. P in New species and records of Pyrgulopsis (Gastropoda: Hydrobiidae) from the Snake River basin, southeastern Oregon: further delineation of a highly imperiled fauna

FIGURE 4. P. fresti sp. nov., USNM 1102161. A. Portion of radula ribbon. Scale bar = 20 µm. B. Central radular teeth. Scale bar = 10 µm. C. Lateral and inner marginal teeth. Scale bar = 10 µm. D. Inner marginal tooth. Scale bar = 10 µm. E. Outer marginal teeth. Scale bar = 10 µm..F. Outer marginal tooth, showing outer wing. Scale bar = 10 µm. Wg = wing.

FIGURE 7. P in New species and records of Pyrgulopsis (Gastropoda: Hydrobiidae) from the Snake River basin, southeastern Oregon: further delineation of a highly imperiled fauna

FIGURE 7. P. owyheensis sp. nov. A–F. Opercula. Scale bar = 500 µm. A–B. Outer side, showing frilled whorls, USNM 1116915, USNM 1092854. C–F. Inner side, showing variation in thickening of attachment scar margin, USNM 1116915, USNM 1102152, USNM 1092854, USNM 1092854. Rm = rim.

FIGURE 1 in New species and records of Pyrgulopsis (Gastropoda: Hydrobiidae) from the Snake River basin, southeastern Oregon: further delineation of a highly imperiled fauna

FIGURE 1. Map showing the distributions of Pyrgulopsis species in southeastern Oregon. Arrows indicate previously documented localities; all others are newly reported herein. Some of the symbols refer to multiple, closely proximal localities.

FIGURE 9. P in New species and records of Pyrgulopsis (Gastropoda: Hydrobiidae) from the Snake River basin, southeastern Oregon: further delineation of a highly imperiled fauna

FIGURE 9. P. owyheensis sp. nov.. A–B. Penis, USNM 1092819. Scale bar = 0.25 mm. A. Dorsal surface. B. Ventral surface. C–D. Penis, USNM 1102152. Scale bar = 0.5 mm. C. Dorsal surface. D. Ventral surface. E. Female glandular oviduct and associated structures (viewed from the left side), USNM 1092819. Scale bar = 0.25 mm. F. Bursa copulatrix and its duct. Scale as in "E." G. Seminal receptacle and its duct. Scale as in "E." Ag = albumen gland, Bu = bursa copulatrix, Cd = common duct of seminal receptacle and coiled oviduct, Cg = capsule gland, Co = coiled oviduct, Dbu = bursal duct, Ga =genital aperture, Pd = penial duct, Pf = penial filament, Pg = penial gland, Pl = penial lobe, Pw = posterior wall of pallial cavity, Sr = seminal receptacle, Tg = terminal gland, Vc = ventral channel, Vg = ventral gland.