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Figures 14-18. D in Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Figures 14-18. D. jana sp. n. holotype, right male bulb 14 prolateral view, general 15 anterior view 16 posterior view 17 retrolateral view 18 P, prolateral view.

Figures 19-22. D. shardana holotype, right male bulb 19 prolateral view, general 20 prolateral view, tip detail 21 anterior view 22 P in Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Figures 19-22. D. shardana holotype, right male bulb 19 prolateral view, general 20 prolateral view, tip detail 21 anterior view 22 P, prolateral view.

Figures 8-9 in Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Figures 8-9. Left male palp, retrolateral view: 8 D. jana sp. n. holotype 9 D. shardana sp. n. holotype.

Figures 10-13. D in Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Figures 10-13. D. jana sp. n. paratype female 10 vulva, dorsal view 11 vulva, ventral view. D. shardana sp. n. paratype female 12 vulva, dorsal view 13 vulva, ventral view.

Figure 1 in Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Figure 1. Maps showing the location of Sardinia and known localities of the new species. Dysdera jana sp. n.: Nuoro: 1 Dorgali, 450 m, 2 2 km S of Dorgali, 500 m, 3 Supramonte di Oliena, 900 m, 4 Sa Oche, 7 km ESE of Oliena, 150 m. D. shardana sp. n.: Cagliari: 5 Fluminimaggiore, Is Arenas, 6 Flu- minimaggiore, Tempio di Antas, Nuoro: 7 Aritzo, Castagneto Geratzia, 867 m, 8 Desulo, rd. to Fonni, 1146 m, 9 Macomer, Mt. S. Antonio. Oristano: 10 Cuglieri, rd. to San Leonardo 7 Fuentes, 587 m, 11 S. Leonardo 7 Fuentes, 699 m, 12 Morgongiori, Is Benas recreation area, 566 m, 13 Morgongiori, Bruncu Mutzuis, 761 m, 14 Sassari: NW Torralba.

Figures 4-7 in Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Figures 4-7. Carapace, dorsal view: 4 D. jana sp. n. holotype 5 D. shardana sp. n. holotype. Carapace, lateral view: 6 D. jana sp. n. holotype 7 D. shardana sp. n. holotype.

Figure 3 in Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Figure 3. Haplotype network constructed using statistical parsimony (95%). Dots on branches refer to missing haplotypes. Node size proportional to number of haplotypes (1 or 2), nodes colour code and numbers inside refer to localities in Fig. 1.

opencc-by-4.0Aug 2015View details →

Figure 4 in Phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the boreal island of Hokkaido, Japan

Figure 4. Network of the 29 cytochrome b gene haplotypes of Sciurus vulgaris orientis in Hokkaido Island, Japan, using statistical parsimony. Haplotype names correspond to Appendix 1. Missing haplotypes are indicated by open circles. Lines connecting haplotypes indicate the relationship. Numbers in parentheses indicate the number of individuals. Haplotypes without parentheses are from just one individual.

opencc-by-4.0Aug 2015View details →

Figure 5 in Phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the boreal island of Hokkaido, Japan

Figure 5. Observed (solid lines with solid diamonds) and expected (dotted lines with open squares) mismatch distributions of Sciurus vulgaris orientis haplotypes: A) northern population; B) southern population; C) over all of Hokkaido population.

opencc-by-4.0Aug 2015View details →

Figure 3 in Phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the boreal island of Hokkaido, Japan

Figure 3. Phylogeny of Sciurus vulgaris constructed with the Bayesian inference (BI) under a HKY + G model for the cytochrome b sequences. Numbers above branches represent posterior probability supports in Bayesian analysis followed by bootstrap values from 300 replicates of ML analysis. Hyphens mean no data because clades were absent. Symbols indicate phylogroups, and correspond to those in Figure 2.

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Data from: Full Bayesian comparative phylogeography from genomic data

A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data. By analytically integrating over gene trees, we are able to directly calculate the likelihood of the population history from genomic data, and efficiently sample the model-averaged posterior via Markov chain Monte Carlo algorithms. Using simulations, we find that the new method is much more accurate and precise at estimating the number and timing of divergence events across pairs of populations than existing approximate-likelihood methods. Our full Bayesian approach also requires several orders of magnitude less computational time than existing ABC approaches. We find that despite assuming unlinked characters (e.g., unlinked single-nucleotide polymorphisms), the new method performs better if this assumption is violated in order to retain the constant characters of whole linked loci. In fact, retaining constant characters allows the new method to robustly estimate the correct number of divergence events with high posterior probability in the face of character-acquisition biases, which commonly plague loci assembled from reduced-representation genomic libraries. We apply our method to genomic data from four pairs of insular populations of Gekko lizards from the Philippines that are not expected to have co-diverged. Despite all four pairs diverging very recently, our method strongly supports that they diverged independently, and these results are robust to very disparate prior assumptions.

opencc-zeroDec 2017View details →

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Phylogeography of lionfishes (Pterois) indicate taxonomic over splitting and hybrid origin of the invasive Pterois volitans

The evolutionary consequences of hybridization are poorly understood, especially in the marine realm where hybridization was once thought to be a rare occurrence. Previous research indicated that the lionfishes Pterois volitans and P. miles are sister species, both of which have been detected in the recent invasion of the Atlantic. Anecdotal data from the invasive range indicates they may hybridize, but previous studies have not examined the potential for these species to hybridize in the native range, or how such hybridization affects the distribution of genetic diversity. Here we address evolutionary divergence and population structure using mtDNA COI and two nuclear introns from 214 lionfish including four putative sister species (36 P. miles, 90 P. volitans, 32 P. lunulata, and 56 P. russelii) collected at 10 locations. Genetic data are supplemented with a re-examination of key morphological characters: dorsal, anal and pectoral fin ray counts. These data reveal two lineages (d = 0.041 in COI) among the four putative species: an Indian Ocean lineage, represented by P. miles and a Pacific Ocean lineage represented by P. lunulata and P. russelii. Lionfish identified as P. volitans appear to be hybrids between the sister linages of P. miles and P. lunulata/russelii, a conclusion supported by both the genetic data and morphology. The degree and geographic extent of introgression indicates widespread hybridization, or the absence of valid species distinctions between all four species. These findings also indicate that the lionfish invading tropical Atlantic Ocean, usually labeled P. volitans, is a hybrid.

opencc-zeroJan 2020View details →

opencc-zeroDec 2016View details →

FIGURE 2 in Flightless litter-dwelling Cotasterosoma (Coleoptera: Curculionidae: Cossoninae) found outside of Japan, with mtDNA phylogeography of a new species from Southwest China

FIGURE 2. Cotasterosoma coronus sp. n., paratype, female, specimen # 1110 from Mt. Emei. A – D: habitus; E – F: head and prothorax (E: ventral, F: lateral); G – I: distal part of right legs (G: fore-, H: mid-, I: hind-); J: genitalia, ventral; K: spermatheca.

opencc-zeroDec 2016View details →

FIGURE 1 in Flightless litter-dwelling Cotasterosoma (Coleoptera: Curculionidae: Cossoninae) found outside of Japan, with mtDNA phylogeography of a new species from Southwest China

FIGURE 1. Cotasterosoma coronus sp. n., holotype, male. A – D: habitus; E: genitalia and abdominal tergites 7 and 8, ventral; F – H: genitalia (F: dorsal, G: ventral, H: lateral).

Fig. 6 in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia

Fig. 6. Distribution and species richness for the eight genera of woody bamboo forests currently found in Asia (adapted and modified from Bystriakova et al. 2003b) and putative geographic range areas of the species of Tylonycteris. During glacial periods of the Pleistocene, the highlighted biogeographic regions may have acted as bamboo refugia for Tylonycteris spp. Moreover, sea level falls (at around 120 m below present) exposed land bridges, such as the entire Sunda Shelf (adapted from Voris 2000), connecting the islands to the continent.

Fig. 5 in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia

Fig. 5. Morphological characteristics of the two nominal species of the genus Tylonycteris Peters, 1872. A. T. pachypus (Temminck, 1840) (corrected taxon name is T. fulvida (Blyth, 1859)), IEBR-VN11- 0015. B. T. robustula Thomas, 1915 (corrected taxon name is T. tonkinensis Tu, Csorba, Ruedi & Hassanin sp. nov.), holotype, IEBR-VN11-0055. Head profiles, ventral and dorsal views, fleshy pads at the base of the thumb and on the sole of the foot, and different views of the skull (dorsal, ventral and lateral). Scale = 10 mm.

Fig. 4 in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia

Fig. 4. Scatter plots obtained from morphological analyses of Tylonycteris spp. A. Range of GLS measurements of specimens within each group of Tylonycteris spp. B. Range of PC*1 scores of specimens of Tylonycteris spp. obtained from PCA of log-transformed raw data of craniodental measurements. C. Plot of PC 1 against PC 2 obtained from PCA on log-transformed standardized data. Triangles and circles refer to T. pachypus s. lat. and T. robustula s. lat., respectively. Colour patterns indicate the mtDNA haplogroups: green for Tp3 and Tr3 (northern Indochina); blue for Tp2 and Tr2 (other regions of the Southeast Asian mainland); red for Tp1 and Tr1 (Sundaland).

Fig. 1. A–B in Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia

Fig. 1. A–B. Maps of Asia showing the distribution range (shaded) and type localities of described subspecies of T. pachypus (Temminck, 1840) and T. robustula Thomas, 1915 (Bates et al. 2008a, 2008b). C. Localities of Tylonycteris specimens included in this study. Triangles and circles refer to T. pachypus and T. robustula, respectively; the colours indicate the mtDNA haplogroups found in the Bayesian analyses of COI and Cytb sequences (see Fig. 2 for details).