A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient

Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Sarcocystis scandentiborneensis sp. nov. was discovered in histological sections of striated musculature of treeshrews (Tupaia minor, T. tana) from Northern Borneo. Sarcocysts were cigar-shaped, 102 μm–545 μm long, and on average 53 μm in diameter. The striated cyst wall varied in thickness (2–10 μm), depending on whether the finger-like, villous protrusions (VP) were bent. Ultrastructurally, sarcocysts were similar to wall type 12 but basal microtubules extended into VPs that tapered off with a unique U-shaped, electron-dense apical structure. In phylogenetic trees of the nuclear 18S rRNA gene, S. scandentiborneensis formed a distinct branch within a monophyletic subclade of Sarcocystis spp. with (colubrid) snake-rodent life cycle. We mapped all intraspecific (two haplotypes) and interspecific nucleotide substitutions to the secondary structure of the 18S rRNA gene: in both cases, the highest variability occurred within helices V2 and V4 but intraspecific variability mostly related to transitions, while transition/transversion ratios between S. scandentiborneensis, S. zuoi, and S. clethrionomyelaphis were skewed towards transversions. Lack of relevant sequences restricted phylogenetic analysis of the mitochondrial Cytochrome C oxidase subunit I (COI) gene to include only one species of Sarcocystis recovered from a snake host (S. pantherophisi) with which the new species formed a sister relationship. We confirm the presence of the functionally important elements of the COI barcode amino acid sequence of S. scandentiborneensis, whereby the frequency of functionally important amino acids (Alanine, Serine) was markedly different to other taxa of the Sarcocystidae. We regard S. scandentiborneensis a new species, highlighting that structurally or functionally important aspects of the 18S rRNA and COI could expand their utility for delineation of species. We also address the question why treeshrews, believed to be close to primates, carry a parasite that is genetically close to a Sarcocystis lineage preferably developing in the Rodentia as intermediate hosts

Euarchontan opsin variation brings new focus to primate origins

Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, i.e., the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination

Whipworms of south-east Asian rodents are distinct from Trichuris muris

The whipworm Trichuris muris is known to be associated with various rodent species in the northern hemisphere, but the species identity of whipworm infecting rodents in the Oriental region remains largely unknown. We collected Trichuris of Muridae rodents in mainland and insular Southeast Asia between 2008 and 2015 and used molecular and morphological approaches to identify the systematic position of new specimens. We discovered two new species that were clearly distinct from T. muris, both in terms of molecular phylogenetic clustering and morphological features, with one species found in Thailand and another one in Borneo. We named the new species from Thailand as Trichuris cossoni and the species from Borneo as Trichuris arrizabalagai. Molecular phylogeny using internal transcribed spacer region (ITS1-5.8S-ITS2) showed a divergence between T. arrizabalagai n. sp., T. cossoni n. sp. and T. muris. Our findings of phylogeographically distinct Trichuris species despite some globally distributed host species requires further research into the distribution of different species, previously assumed to belong to T. muris, which has particular relevance for using these species as laboratory model organisms

Phortica (Phortica) gombakana

Phortica (Phortica) gombakana (Takada & Momma, 1975) Amiota (Phortica) gombakana Takada & Momma, 1975: 14. Diagnosis. – Vertical process of gonopods with spinules apicomedially; aedeagus with 2 pairs of bridges, of which the ventral pair is strongly sclerotized. Material examined. – Holotype male, MALAYSIA: Gombak, near Kuala Lumpur, coll. H. Takada, 4 Jul.1972 (SEHU); Ulu Senagang, Crocker Range, Sabah, 1 male, coll. M. J. Toda, 18 Oct.1999 (KPSP). Distribution. – Malaysia (Malaya, Sabah).Published as part of Chen, Hong-Wei, Toda, Masanori J., Lakim, Maklarin B. & Mohamed, Maryati B., 2007, The Phortica Sensu Stricto (Insecta: Diptera: Drosophilidae) From Malaysia, pp. 23-41 in Raffles Bulletin of Zoology 55 (1) on pages 28-29, DOI: 10.5281/zenodo.533304

Phortica (Phortica) jamilii Chen & Toda & Lakim & Mohamed 2007, new species

Phortica (Phortica) jamilii Chen & Toda, new species (Figs. 11–15) Diagnosis. – Aedeagal median rod subapically with 1 pair of long slender projections and submedially with 1 pair of long, broad, apically bifurcated projections (Fig. 15). Material examined. – Holotype male (terminalia dissected), MALAYSIA: Park Headquarters, Mt. Kinabalu, Sabah, coll. M. J. Toda, 20 Mar.1999 (KPSP). Paratype: 1 male (terminalia dissected), same data as the holotype except for 7 Mar.2000 (SEHU). Description. – Male. Head: Frons brown with large triangular black patch on upper half. Thorax: Orange yellow. Scutellum with trifurcate brown patch, yellowish white on tip. Wing: Slightly smoky. Legs: All femora almost brown. Midleg tibia subapically lacking longer setae on anterior surface. Abdomen: First to fifth tergites yellow; second tergite with black patches submedially and laterally; third tergite with medially and laterally slightly protruded, sublaterally nearly interrupted, brown band on posterior margin; fourth and fifth tergites each with medially and laterally slightly protruded, brown band on posterior margin and 1 pair of small yellow patches sublaterally; sixth tergite nearly entirely black except yellow medial line, extended below at posterolateral corners (Fig. 11). Male terminalia: Epandrium pubescent anteroventrally and dorsomedially, with ca. 14-15 setae near dorsal to posterolateral margin per side (Fig. 12). Surstylus pubescent basally, with several wedge-shaped prensisetae on apical margin to inner surface (Fig. 13). Additional plate between cerci and 10th sternite pubescent, medially connected to 10th sternite (Fig. 14). Posterolateral lobe of hypandrium large, lacking pubescence (Fig. 15). Paramere lacking pubescence; apical process with 3 teeth apically and 1 sensillum subapically; median process triangular; proximal process slender, with 1 sensillum apically (Fig. 15). Vertical process of gonopods triangular lobe-like (Fig. 15). Aedeagal median rod subbasally with 1 pair of small processes; outer membranous tube convoluted apically, with transparent minute spinules subapically and basally (Fig. 15). Aedeagus with 1 pair of looped bridges basally (Fig. 15). Female: Unknown. Measurements: BL = 4.20 mm in holotype (1 male paratype: 4.18); ThL = 1.94 mm (1.83); WL = 3.20 mm (3.08); WW = 1.36 mm (1.28). Indices: arb = 3-4/2-3 (3-4/2-3), avd = 0.67 (0.70), adf = 1.45 (1.50), flw = 1.30 (1.40), FW/HW = 0.38 (0.35), ch/o = 0.06 (0.06), prorb = 1.00 (1.00), rcorb = 0.55 (0.60), vb = 0.35 (0.30), dcl = 0.55 (0.60), presctl = 0.60 (0.60), sctl = 1.00 (1.00), sterno = 0.90 (0.95), orbito = 1.30 (1.30), dcp = 0.25 (0.25), sctlp = 1.00 (1.00), C = 2.25 (2.20), 4c = 1.67 (1.60), 4v = 3.33 (3.00), 5x = 1.13 (1.10), ac = 5.00 (4.80), M = 0.75 (0.73), C3F = 0.70 (0.70). Etymology. – Patronym, in honor of Dr. Jamili Nais of the Sabah Parks, Malaysia. Distribution. – Malaysia (Sabah). Remarks. – This species is similar to P. (P.) eugamma (Toda & Peng, 1990) from southern China in the pattern of abdominal tergites, but can be distinguished from it by the aedeagal median rod (in P. eugamma: aedeagal median rod subapically with 1 single, submedially with 1 paired, small, simple projections).Published as part of Chen, Hong-Wei, Toda, Masanori J., Lakim, Maklarin B. & Mohamed, Maryati B., 2007, The Phortica Sensu Stricto (Insecta: Diptera: Drosophilidae) From Malaysia, pp. 23-41 in Raffles Bulletin of Zoology 55 (1) on page 29, DOI: 10.5281/zenodo.533304

Phortica Schiner 1862

Key to the species of the subgenus Phortica from Malaysia 1. Interfrontal setae thick and dense; additional plate between cerci and 10th sternite absent; paramere rod-shaped, basally mostly projected and with a few sensilla, apically usually knobbed (the foliiseta species-complex)..................................................... 2 – Interfrontal setae thin and rare; additional plate between cerci and 10th sternite present; paramere apically with a few sensilla............................................................................................... 3 2. Surstylus with only 2–3 prensisetae; vertical process of gonopods nearly entirely sclerotized apically; aedeagal outer membrane with minute warts.......... P. (P.) nigrifoliiseta (Takada et al.) – Surstylus with ca. 11 prensisetae; vertical process of gonopods slightly sclerotized; aedeagal outer membrane with numerous, weakly sclerotized, small triangle processes.............................................................................. P. (P.) tanabei Chen & Toda 3. Surstylus with strong spine(s); additional plate between cerci and 10th sternite lacking pubescence, separated from 10th sternite (the magna species-complex)..................................................................... P. (P.) alpha Chen & Toda, new species – Surstylus without strong spine; additional plate between cerci and 10th sternite pubescent, and connected to 10th sternite................................................................................................... 4 4. Paramere deeply bifurcated from base (the omega speciescomlpex); male sixth tergite with single prickly projection curved anteriod at anteroventral corner; lateral process of paramere narrower than and ca. 2/3 as long as apical one, apically with 1 sensillum and 1 black spine........................................................................................... P. (P.) ni Chen & Toda, new species – Paramere not bifurcated from base....................................... 5 5. Paramere tripartite distally.................................................... 6 – Paramere not tripartite distally........................................... 13 6. Paramere: basal process with tooth or sensillum; median process tongue- or finger-shaped, without tooth or sensillum.......... 7 – Paramere: basal process tongue- or finger-shaped; median process apically with tooth and sensillum............................ 9 7. Aedeagal median rod lacking projections................................................................ P. (P.) gombakana (Takada & Momma) – Aedeagal median rod with apically pointed projection(s)... 8 8. Aedeagal median rod subapically and submedially with 1 pair of small and 1 pair of long, apically bifurcated projections, respectively................................. P. (P.) jamilii, new species – Aedeagal median rod submedially with 2 pairs of apically unbifurcated projections............................................................................................. P. (P.) liewi Chen & Toda, new species 9. Vertical process of gonopods broad, largely membranous except for medial and lateral, strongly sclerotized portions; aedeagal ventral bridge strongly sclerotized, elongated to tip of aedeagal median rod, pointed apically, with large branch submedially..................... P. (P.) membranifera Chen & Toda, new species – Vertical process of gonopods basally to submedially narrow and evenly sclerotized................................................................ 10 10. Aedeagal basal bridge with somewhat triangular flap acutely pointed only anterodorsally................................................................................. P. (P.) expansa Chen & Toda, new species – Aedeagal basal bridge with flap acutely pointed antero- and mediodorsally...................................................................... 11 11. Aedeagal median rod with subbasal process................................................... P. (P.) pasohensis Chen & Toda, new species – Aedeagal median rod with submedial process................... 12 12. Aedeagal basal bridge with long, sclerotized, apically pointed projection anteroventrally; ventral bridge apically somewhat truncate....... P. (P.) kinabalensis Chen & Toda, new species – Aedeagal basal bridge without long projection anteroventrally; ventral bridge apically largely bifurcated............................................................. P. (P.) palmata Chen & Toda, new species 13. Anepisternum lacking setulae; paramere lacking pubescence; aedeagal median rod apically with distinct asymmetric bifurcation, subapically expanded and with minute warts on surface................. P. (P.) epsilon Chen & Toda, new species – Anepisternum with setulae................................................. 14 14. Paramere medially not expanded, distally pubescent; aedeagal median rod with knot subapically; anterior branch of aedeagal basal bridge with ca. 10 acute projections along margin................................ P. (P.) lanuginosa Chen & Toda, new species – Paramere medially much expanded, submedially pubescent; aedeagal median rod much expanded subapically; aedeagal basal bridge without small acute projections....................................................................... P. (P.) zeta Chen & Toda, new speciesPublished as part of Chen, Hong-Wei, Toda, Masanori J., Lakim, Maklarin B. & Mohamed, Maryati B., 2007, The Phortica Sensu Stricto (Insecta: Diptera: Drosophilidae) From Malaysia, pp. 23-41 in Raffles Bulletin of Zoology 55 (1) on page 40, DOI: 10.5281/zenodo.533304

Phortica (Phortica) pasohensis Chen & Toda 2007, new species

Phortica (Phortica) pasohensis Chen & Toda, new species (Figs. 50–53) Diagnosis. – Aedeagal median rod subbasally with single, apically symmetrically bifurcated process (Fig. 53); aedeagal ventral bridge distally expanded (Fig. 53); aedeagal basal bridge with small flap bearing 2 acute projections anteriorly and medioventrally (Fig. 53). Material examined. – Holotype male, MALAYSIA: Pasoh, Selangor, Malaya, coll. N. Osawa, 2–9 May.1995 (FRIM). Decription. – Male. Thorax: Orange yellow. Scutellum with trifurcate brown patch, pale yellow on tip. Wing: Hyaline. Legs: All femora partly brown. Midleg tibia subapically with 2-4 longer setae on anterior surface. Abdomen: First to fifth tergites yellow; second tergite with brown patches submedially; third to fifth tergites each with medially slightly protruded, brown band on posterior margin and 1 pair of yellow patches laterally; sixth tergite nearly entirely dark except yellow medial line, with expanded lobe on lateral margin. Male terminalia: Epandrium pubescent anteroventrally and dorsomedially, with ca. 12 setae on dorsal to posterolateral portion per side (Fig. 50). Surstylus with pubescence basally and several wedge-shaped prensisetae on apical margin to inner surface (Fig. 51). Additional plate between cerci and 10th sternite pubescent, medially connected to 10th sternite (Fig. 52). Posterolateral lobe of hypandrium undeveloped. Paramere expanded distally, pubescent between medial and proximal processes; apical process with 1 sensillum; medial process with 1 sensillum and 2 teeth (Fig. 53). Vertical process of gonopods apically with 4-5 sclerotized projections per side (Fig. 53). Aedeagus with 2 pairs of bridges (Fig. 53). Female: Unknown. Measurements: BL = 3.47 mm in holotype; ThL = 1.76 mm; WL = 2.60 mm; WW = 1.24 mm. Indices: arb = 5-6/3-4, avd = 0.60, adf = 1.80, flw = 1.70, FW/HW = 0.38, ch/o = 0.06, prorb = 1.10, rcorb = 0.45, vb = 0.45, dcl = 0.65, presctl = 0.70, sctl = 1.05, sterno = 0.85, orbito = 1.40, dcp = 0.23, sctlp = 1.10, C = 1.90, 4c = 1.67, 4v = 2.67, 5x = 1.33, ac =4.00, M = 0.67, C3F = 0.70. Etymology. – Pertaining to the type locality. Distribution. – Malaysia (Malaya). Remarks. – This species is very similar to P. (P.) expansa in the morphology of male terminalia, but can be distinguished from it by the diagnostic characters.Published as part of Chen, Hong-Wei, Toda, Masanori J., Lakim, Maklarin B. & Mohamed, Maryati B., 2007, The Phortica Sensu Stricto (Insecta: Diptera: Drosophilidae) From Malaysia, pp. 23-41 in Raffles Bulletin of Zoology 55 (1) on pages 37-38, DOI: 10.5281/zenodo.533304

Phortica (Phortica) magna

II. Phortica (Phortica) magna species-complex Amiota (Phortica) magna species-complex, Chen & Toda, 1997: 785. Diagnosis. – Surstylus with black, thick spine-like prensisetae (Fig. 3); additional plate between cerci and 10th sternite lacking pubescence, separated from 10th sternite (Fig. 4); paramere foliate (Fig. 5); aedeagus basolaterally with 1 pair of seemingly looped processes (Fig. 5).Published as part of Chen, Hong-Wei, Toda, Masanori J., Lakim, Maklarin B. & Mohamed, Maryati B., 2007, The Phortica Sensu Stricto (Insecta: Diptera: Drosophilidae) From Malaysia, pp. 23-41 in Raffles Bulletin of Zoology 55 (1) on page 25, DOI: 10.5281/zenodo.533304

Phortica (Phortica) nigrifoliiseta

Phortica (Phortica) nigrifoliiseta (Takada, Momma & Shima, 1973) Amiota (Phortica) nigrifoliiseta Takada, Momma & Shima, 1973: 74; Tsacas & Okada, 1983: 236. Diagnosis. – Surstylus with 2–3 peg-like prensisetae; vertical process of gonopods nearly entirely sclerotized apically; paramere finely serrated apically; aedeagal outer membrane with minute warts. Material examined. – MALAYSIA: 1 male paratype, Mt. Kinabalu, Sabah, coll. H. Takada, 28 Jun.1972 (SEHU). Distribution. – Malaysia (Sabah).Published as part of Chen, Hong-Wei, Toda, Masanori J., Lakim, Maklarin B. & Mohamed, Maryati B., 2007, The Phortica Sensu Stricto (Insecta: Diptera: Drosophilidae) From Malaysia, pp. 23-41 in Raffles Bulletin of Zoology 55 (1) on page 25, DOI: 10.5281/zenodo.533304