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FIGURE 7 in Molecular phylogenetics and taxonomy of dwarf hamsters Cricetulus Milne-Edwards, 1867 (Cricetidae, Rodentia): description of a new genus and reinstatement of another
FIGURE 7. Occlusal view of M1 and M2; (a) Cricetulus barabensis (ZMMU S-187357), (b) Cricetulus longicaudatus (ZMMU S-187364), (c) Nothocricetulus migratorius (ZMMU S-15931), (d) Urocricetus aff.alticola (ZMMU S-155362), (e) Allocricetulus eversmanni (ZMMU S-171981). Arrow рoints to the median mure.
FIGURE 6 in Molecular phylogenetics and taxonomy of dwarf hamsters Cricetulus Milne-Edwards, 1867 (Cricetidae, Rodentia): description of a new genus and reinstatement of another
FIGURE 6. Ventro-lateral view of the auditory bulla; (a) Cricetulus longicaudatus (ZMMU S-63115), (b) Urocricetus aff.alticola (ZMMU S-155360).
FIGURE 1 in An extinct hummingbird species that never was: a cautionary tale about sampling issues in molecular phylogenetics
FIGURE 1. (A) Distributions of Aglaiocercus kingii, A. coelestis, and Taphrolesbia griseiventris (polygons), and geographic provenance of specimens of these species and of the Rogitama hybrid hummingbird included in molecular analyses (dots and star). (B) Phylogenetic relationships among species and populations of Aglaiocercus, Taphrolesbia, the Rogitama hummingbird, and Heliangelus zusii based on sequences of the ND2 gene. Black dots indicate strongly supported nodes (0.95 Bayesian posterior probability,> 80% maximum-likelihood bootstrap). The Rogitama hummingbird and H. zusii have haplotypes closely allied to those of A. kingii from the Eastern Cordillera of Colombia, indicating they are hybrids sharing A. kingii as female parent. Sister taxon, Adelomyia melanogenys, and outgroup Chalcostigma herrani, are not shown. Illustrations courtesy of Lynx Edicions (del Hoyo et al. 2018).
FIGURE 1. The phylogenetic relationships among Acaenitinae species inferred from a 590 in Two new species of the genus Ishigakia (Hymenoptera: Ichneumonidae, Acaenitinae) from Vietnam based on morphological and molecular evidence
FIGURE 1. The phylogenetic relationships among Acaenitinae species inferred from a 590bp fragment of the COI gene based on Maximum Likelihood, Bayesian Inference analyses. Values at nodes are bootstrap or BI. #: values less than 65 or 0.65.
FIGURE 2 in An extinct hummingbird species that never was: a cautionary tale about sampling issues in molecular phylogenetics
FIGURE 2. Correlation between genetic divergence (p and Tamura-Nei distances) based on the small fragment available for Heliangelus zusii (fragment) with divergence in complete sequences (ND2 gene) across 315 hummingbird taxa (McGuire et al. 2014 dataset). Genetic distances were calculated in MEGA6 (Tamura et al. 2013) and all positions with missing data were not considered when calculating pairwise genetic distances. The plot is cropped at 10% p-distance, thus providing a better view of the data spread in the area of low divergence relevant to the H. zusii issue. The correlation between the small fragment available for H. zusii and all the ND2 data is strong, and it is especially tight near the origin: 0% divergence in that small fragment essentially means no (or up to approximately 1%) divergence in the rest of the sequence. This suggests that our observation of identical sequences in H. zusii and A. kingii is not an artifact resulting from the small amount of available sequence data.
FIGURE 1 in Taxonomic revisions within Embiotocidae (Teleostei, Perciformes) based on molecular phylogenetics
FIGURE 1. Molecular phylogeny of Embiotocidae inferred using genome wide RADseQ markers with maXimum likelihood and Bayesian methods (Longo & Bernardi 2015) with the following proposed taXonomic revisions; resurrecting Hypsurus caryi (Agassiz 1853) to its original name Embiotoca caryi, moving Rhacochilus vacca (Girard 1855) into the genus Phanerodon, and separating Hyperprosopon anale Agassiz 1861 into the available genus Hypocritichthys. Note: The Western Pacific genus Ditrema includes two other valid species not present in this figure, D. viride and D. jordani; see Katafuchi et al. (2010) for proposed interspecific relationships in this genus. Top and bottom node values represent posterior probability and bootstrap support, respectively.
FIGURE 16 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 16. Evolution of habitat usage among Phrynocephalus species and populations including outgroups. Rock habitat is only used by the outgroup Laudakia. Hard substrates are clay, gravel, and dry lakebed. Soft substrates are small sand dune and large sand dune. See table 5 and the methods section for details of habitat categories, and plates I–VIII for images of habitats with species.
FIGURE 15. Maximum glaciation 18,000 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 15. Maximum glaciation 18,000 years before present. Much of northern Asia was never fully glaciated, unlike most of high-latitude North America and Europe, lending the possibility of an old history in the north. The map is redrawn from McIntrye et al. (1976).
FIGURE 13 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 13. Late Miocene (6.0–5.5 MYBP) with the Caspian Basin, Black Sea and Mediterranean Sea as evaporitic regions. The minimal extent of water in the Caspian Basin may have promoted dispersal events among Phrynocephalus populations. The map is after Steininger & Rogl (1984).
FIGURE 12 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 12. Tectonic setting for the formation of mountain belts in central and Southwest Asia at 10 MYBP, Late Miocene. The map is after Dercourte et al. (1986) and uplifting in the Pamir and Karakoram mountains is schematic after Tapponier et al. (1981). Tectonic processes depicted here continue today. During the late Miocene (10 MYBP, Tortonian), India wedged deeply into Eurasia, and Arabia began indentation into Iran (composed of Cimmerian Plates). The Pamir Mountains were experiencing intense uplifting during the Late Miocene (10 MYBP). The indentation of Arabia into Iran in the Late Miocene (10 MYBP) began the formation of the Zagros Mountains in the southern part of the Iranian Plateau. In the northern part of the Iranian Plateau, the Lesser Caucasus Mountains and Kopet-Dagh began uplifting in the early Pliocene (5 MYBP). Plates are labeled in capital letters and ancient Gondwanan Plates (Cimmerian Plates) are Iran (Lut), Farah, and Helmand. Note that the indentations of both India and Arabia are compressing the Cimmerian Plates and causing intense mountain building along paleo-sutures of these plates.
FIGURE 10 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 10. Tectonic setting for the formation of mountain belts in central and Southwest Asia at 35 MYBP, Eocene/ Oligocene. The map is after Dercourte et al. (1986). Note the approaching Arabian Plate, with much of Southwestern Asia in front of the Indian Plate.
FIGURE 9 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 9. Movements of tectonic plates. During the middle Eocene, 50–45 MYBP, India first contacted Eurasia. Since that time, India and Laurasian plates have converged 2365 km in the west, 2475 in the center, and 2750 km in the east (Dewey et al. 1989; Molnar et al. 1987; Royden et al. 2008; Windley 1988). The high altitudes now present in the Hindu Kush, Karakoram, Tien Shan, and Pamir are attributed to the Indian collision (Dewey et al. 1988, 1989). The Hindu Kush between the Helmand and Farah blocks is associated with the uplift of the trans-Himalaya, which includes the Karakoram and is one of the earlier uplifting events. The Tien Shan and Pamir, which now separate the Taklimakan Desert (Tarim Plate) from the Caspian Basin and Farah Block, were formed approximately 10 MYBP (Abdrakhmatov et al. 1996; Tapponier et al. 1981). Crustal shortening and deformation rates are from Dewey et al. (1989). The map is modified from Tapponier et al. (1981).
FIGURE 7 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 7. Strict consensus of 18 equally parsimonious trees of 408 steps from the 25 (all informative) allozyme loci, coded using allele combinations and analyzed with step matrices. Bootstrap values are presented above branches and decay indices are presented below branches in bold. Outgroups (Laudakia, and Trapelus), and well-supported Phrynocephalus clades and lineages discovered in the mitochondrial DNA analysis are identified to the right as D–M where sampling overlaps (clades that are broken are numbered as in Figs. 5 and 6).
FIGURE 6 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 6. Strict consensus of six equally parsimonious trees of 381 steps from the 213 (107 informative) allozyme alleles, coded as presence/absence. Bootstrap values are presented above branches and decay indices are presented below branches in bold. Outgroups (Laudakia, and Trapelus), and well-supported Phrynocephalus clades and lineages discovered in the mitochondrial DNA analysis are identified to the right as D–M where sampling overlaps (clades that are broken are numbered as in Fig. 5).
FIGURE 14 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 14. Pliocene (3.5–3.0 MYBP) extent of the rejuvinted Paratethys Sea. Note that the Caspian Basin is reconnected with the Black Sea and Mediterranean Sea. This period of water inundation may have further subdivided populations of Phrynocephalus. Note the rejuvenated inundation to the southeast of the current Caspian Sea outline, which is at the base of the Kopet-Dagh (mountains) uplifting that initiated approximately 5 MYBP (Smit et al. 2013). The map is after Steininger & Rogl (1984).
FIGURE 5 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 5. Strict consensus of 62 equally parsimonious trees of 831 steps from the 2760 (342 informative) aligned nuclear RAG-1 DNA positions. Bootstrap values are presented above branches and decay indices are presented below branches in bold. Outgroups (Laudakia, Bufoniceps, and Trapelus), and well-supported Phrynocephalus clades and lineages discovered in the mitochondrial DNA analysis are identified to the right as A–M (clades that are broken are numbered).
FIGURE 3. A in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 3. A simplified tectonic map of Asia's associated tectonic plates. Top: The tectonic history of Asia including the break up of Gondwana, trans-Tethys migration of microplates, the isolation of the Indian plate, and subsequent docking of India with Asia (after Tapponier et al. 1981). Bottom: Major plates and suture zones of Asia: low elevations plates of China, J= Junggar and Ta= Tarim; high elevation plates of Tibet, K= Kunlun, Q= Qiangtang and Ti= South Tibet; Southwest Asian plates, F= Farah, H= Helmand, L= Lut, and M= Makran which is an uplift from the Gulf of Oman. Note the complex shifting of plates deep in Asia by Arabia, India, and SE Asia.
FIGURE 2 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 2. The approximate distribution of Phrynocephalus and Bufoniceps laungwalaensis. The 29 Phrynocephalus species sampled are indicated with general geographic distribution. Multiple populations were sampled from 10 species which are: P. arabicus, P. forsythii, P. luteoguttatus, P. maculatus, P. mystaceus, P. przewalskii, P. roborowskii, P. salenskyi, P. scutellatus, and P. vlangalii. Two populations are included from all of the above except for P. przewalskii which is four populations, and P. vlangalii which is three populations. In some cases these are depicted on the map. See appendix 1 for exact localities of samples.
FIGURE 1 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 1. The major deserts of Asia and intervening mountain belts. Major deserts are labeled 1–7 which are: (1) Arabian, (2) Thar, (3) Southwest Asian, (4) Caspian Basin, (5) Gobi-Taklimakan, (6) Qaidam-Qinghai, and (7) High Elevation Tibetan. Intervening mountain belts are labeled A–J which are: (A) Zagroz, (B) Kopet-Dagh, (C) Hindu Kush, (D) Karakorum, (E) Himalaya, (F) Pamir, (G) Tien Shan, (H) Arjin-Qilan, (I) Kunlun, and (J) Tangula Shan. Phrynocephalus species occur in all major desert regions of Asia, with the exception of the Thar Desert in India having Bufoniceps laungwalaensis, which was originally described as a Phrynocephalus species (Sharma 1978) and is the sister taxon to Trapelus (Macey et al. 2006).
FIGURE 17 in A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics
FIGURE 17. Highest maximum-likelihood tree (-ln = 19894.22) from the 1595 included aligned mitochondrial DNA positions. Bootstrap values are presented above branches and comparative parsimony decay indices are presented below branches in bold (Macey 2005). Branches that appear in parsimony analyses have the parsimony decay index plotted. Branches with no parsimony cost but are not present in strict consensus trees are listed as a "0" decay value. Branches that conflict with the parsimony analysis have a negative decay value representing the number of parsimony steps cost to obtain the maximumlikelihood branch. Bold italic bootstraps are those that differ from parsimony analysis. Outgroups (Laudakia, Bufoniceps, and Trapelus), and Phrynocephalus clades and lineages previously identified are labeled to the right as A–M.
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