Friday, August 26, 2016

[Ornithology • 2016] Genomic Variation Across the Yellow-rumped Warbler (Setophaga coronata) Species Complex

The four forms of Yellow-rumped Warbler, Setophaga coronata, have distinct breeding ranges, with a narrow hybrid zone between Myrtle and Audubon's in western Canada. The researchers suggest that Myrtle, Audubon's and Goldman's are separate species. It's equivocal whether Black-fronted should be treated as a separate species or a subspecies of Audubon's. 
Image by David Toews.    

Populations that have experienced long periods of geographic isolation will diverge over time. The application of high-throughput sequencing technologies to study the genomes of related taxa now allows us to quantify, at a fine scale, the consequences of this divergence across the genome. Throughout a number of studies, a notable pattern has emerged. In many cases, estimates of differentiation across the genome are strongly heterogeneous; however, the evolutionary processes driving this striking pattern are still unclear. Here we quantified genomic variation across several groups within the Yellow-rumped Warbler species complex (Setophaga spp.), a group of North and Central American wood warblers. We showed that genomic variation is highly heterogeneous between some taxa and that these regions of high differentiation are relatively small compared to those in other study systems. We found that the clusters of highly differentiated markers between taxa occur in gene-rich regions of the genome and exhibit low within-population diversity. We suggest these patterns are consistent with selection, shaping genomic divergence in similar genomic regions across the different populations. Our study also confirms previous results relying on fewer genetic markers that several of the phenotypically distinct groups in the system are also genomically highly differentiated, likely to the point of full species status.

Keywords: evolutionary genomics, hybridization, gene flow, genotyping-by-sequencing, speciation, natural selection

The Myrtle form breeds in eastern and northern North America. The male's white throat distinguishes it from the three other forms, along with other differences.  
Photo by Kelly Colgan Azar via Birdshare.

David P. L. Toews, Alan Brelsford, Christine Grossen, Borja Milá, and Darren E. Irwin. 2016. Genomic Variation Across the Yellow-rumped Warbler Species Complex  [Variación genómica a través del complejo de especies de Setophaga coronata]. The Auk. 133(4); 698-717.  DOI: 10.1642/AUK-16-61.1

'Butterbutt' warbler is likely three different species, DNA reveals via @physorg_com
Goodbye, Yellow-Rump: Will We See A Return To Myrtle And Audubon’s Warblers?

RESUMEN: Las poblaciones que han experimentado largos periodos de aislamiento geográfico se diferenciarán con el paso del tiempo. La aplicación de tecnologías de secuenciación de alto rendimiento para el estudio de los genomas de taxones relacionados ahora nos permite cuantificar a escala fina las consecuencias de esta divergencia s través del genoma. Luego de numerosos estudios emerge un patrón notable: en muchos casos los estimados de diferenciación a través del genoma son fuertemente heterogéneos. Sin embargo, los procesos evolutivos que gobiernan este patrón aún no son claros. En este estudio cuantificamos la variación genómica a través de varios grupos dentro del complejo de especies de Setophaga coronata, un grupo de reinitas de Norte y Centroamérica. Mostramos que la variación genómica es altamente heterogénea entre algunos de los taxones y que las regiones de alta diferenciación son relativamente pequeñas en comparación con otros sistemas de estudio. Encontramos que las agrupaciones de marcadores áltamente diferenciados entre taxones se encuentran en regiones del genoma ricas en genes y también muestran baja diversidad intrapoblacional. Sugerimos que estos patrones son consistentes con un efecto de procesos de selección natural sobre la divergencia genómica en regiones genómicas similares a través de las diferentes poblaciones. Nuestro estudio también confirma resultados previos basados en pocos marcadores genéticos en los que se determinó que muchos de los grupos fenotípicamente distintos en este sistema también están áltamente diferenciados en sus genomas, probablemente al punto en que pueden ser consideradas con el estatus de especie.

Palabras clave: especiación, flujo genético, genómica evolutiva, genotipado por secuenciación, hibridación, selección natural

D. P. L. Toews, A. Brelsford and D. E. Irwin. 2014. Isotopic variation across the Audubon's–Myrtle warbler hybrid zone. Journal of Evolutionary Biology. 27(6); 1179-1191. DOI: 10.1111/jeb.12392 

[PaleoMammalogy • 2016] Arktocara yakataga • A New Fossil Odontocete (Mammalia, Cetacea) from the Oligocene of Alaska and the Antiquity of Platanistoidea

Arktocara yakataga 
Boersma & Pyenson, 2016

Artistic reconstruction of a pod of Arktocara yakataga, swimming offshore of Alaska during the Oligocene, about 25 million years ago, with early mountains of Southeast Alaska in the background. The authors speculate that Arktocara may have socialized in pods, like today's oceanic dolphins, while possessing a much longer snout, like its closest living relative in the freshwater rivers of South Asia.
Linocut print art by Alexandra Boersma


The diversification of crown cetacean lineages (i.e., crown Odontoceti and crown Mysticeti) occurred throughout the Oligocene, but it remains an ongoing challenge to resolve the phylogenetic pattern of their origins, especially with respect to stem lineages. One extant monotypic lineage, Platanista gangetica (the Ganges and Indus river dolphin), is the sole surviving member of the broader group Platanistoidea, with many fossil relatives that range from Oligocene to Miocene in age. Curiously, the highly threatened Platanista is restricted today to freshwater river systems of South Asia, yet nearly all fossil platanistoids are known globally from marine rocks, suggesting a marine ancestry for this group. In recent years, studies on the phylogenetic relationships in Platanistoidea have reached a general consensus about the membership of different sub-clades and putative extinct groups, although the position of some platanistoid groups (e.g., Waipatiidae) has been contested. Here we describe a new genus and species of fossil platanistoid, Arktocara yakataga, gen. et sp. nov. from the Oligocene of Alaska, USA. The type and only known specimen was collected from the marine Poul Creek Formation, a unit known to include Oligocene strata, exposed in the Yakutat City and Borough of Southeast Alaska. In our phylogenetic analysis of stem and node-based Platanistoidea, Arktocara falls within the node-based sub-clade Allodelphinidae as the sister taxon to Allodelphis pratti. With a geochronologic age between ∼29–24 million years old, Arktocara is among the oldest crown Odontoceti, reinforcing the long-standing view that the diversification for crown lineages must have occurred no later than the early Oligocene.

Systematic paleontology

Cetacea Brisson, 1762
Odontoceti Flower, 1867 sensu Fordyce & Muizon, 2001
Platanistoidea (CCN) (node-based version of Fordyce, 1994)
Allodelphinidae (CCN) (node-based version of Barnes, 2006)

Arktocara, gen. nov. 

The skull of Arktocara yakataga on an 1875 ethnographic map of Alaska drawn by William Healey Dall, a broadly trained naturalist who worked for several US government agencies, including the Smithsonian, and honored with several species of living mammals, including Dall's porpoise (Phocoenoides dalli). Near the skull of Arktocara is a cetacean tooth, likely belonging to a killer whale (Orcinus orca), collected by Aleš Hrdlička, a Smithsonian anthropologist who worked extensively in Alaska, and an Oligocene whale tooth collected by Donald Miller, a geologist who worked for the US Geological Survey, and collected the type specimen of Arktocara. Donald Orth's dictionary of Alaskan place names, published by the USGS, bookends the image.
photo: James Di Loreto, Smithsonian 

Definitions. Crown group Platanista refers to the crown clade arising from the last common ancestor of all lineages descending from Platanista, including two subspecies of Platanista gangetica (P. g. gangetica (Lebeck, 1801) and P. g. minor Owen, 1853), as recognized by The Society for Marine Mammology’ Committee on Taxonomy (2015).

Type and only included species: Arktocara yakataga, sp. nov.

Etymology. The name Arktocara derives from the combination of arktos from Greek and cara from Latin, which together signify “the face of the North.” The only preserved material of the type specimen, USNM 214830 consists of the cranium, or its face, and its type locality is the furthest north that a platanistoid has ever been found.

Age. Same as that of the species.
Diagnosis. Same as that of the species.

Arktocara yakataga, sp. nov. (Figs. 2–10 and Table 1)

The skull of Akrtocara yakataga rests on an 1875 ethnographic map of Alaska drawn by William Healey Dall, a broadly trained naturalist who worked for several US government agencies, including the Smithsonian, and honored with several species of living mammals, including Dall's porpoise (Phocoenoides dalli). Near the skull of Arktocara is a cetacean tooth, likely belonging to a killer whale (Orcinus orca), collected by Aleš Hrdlička, a Smithsonian anthropologist who worked extensively in Alaska, and an Oligocene whale tooth collected by Donald Miller, a geologist who worked for the US Geological Survey, and collected the type specimen of Arktocara. Donald Orth's dictionary of Alaskan place names, published by the USGS, bookends the image.
photo: James Di Loreto, Smithsonian  

Holotype. USNM 214830, consisting of an incomplete skull lacking the rostrum anterior of the antorbital notches, tympanoperiotics, dentition and mandibles (see Fig. 2).

Type locality. The precise geographic coordinates for the type locality of Arktocara yakataga are unknown. The type specimen (USNM 214830) was discovered and collected in 1951 by United States Geological Survey (USGS) geologist Donald J. Miller (1919–1961), who was mapping what was then the Yakataga District of Alaska (now the Yakutat City and Borough) between 1944 and 1963. Archival notes housed with the specimen at USNM state that Miller found the specimen in the Poul Creek Formation within the then-Yakataga District (see Age, below). Therefore, we delimit the area for the type’s provenance to exposures of the Poul Creek Formation in the Yakutat City and Borough, Alaska, USA, in a grid ranging approximately from 60°22′N, 142°30′W to 60°00′N, 143°22′W (see Fig. 1). While the formation has been named from its exposures along Poul Creek, it has been suggested that the most abundant macrofossils from this unit have been collected from outcrops along Hamilton Creek, White River, and Big River near Reare Glacier (Taliaferro, 1932). It is possible that Miller collected USNM 214830 from one of these exposures.

Formation. Poul Creek Formation.

Age. Archival documentation accessioned in the Department of Paleobiology with USNM 214830 indicate that the type specimen was collected from an unknown locality exposed about 400–500 m below the top of the Poul Creek Formation, which has a total stratigraphic thickness of around 1.9 km (Plafker, 1987). The Yakutat terrane of Southeast Alaska consists of the Kulthieth, Poul Creek, and Yakataga Formations (Perry, Garver & Ridgway, 2009; Plafker, Moore & Winkler, 1994; Miller, 1971). The Kulthieth Formation consists of mostly organic-rich sandstones deposited in nonmarine alluvial, deltaic, barrier beach and shallow marine environments, and is Early Eocene to Early Oligocene (∼54–33 Ma) in age based on the fossil assemblages present (Perry, Garver & Ridgway, 2009). The Upper Eocene to possibly Lower Miocene (∼40–20 Ma) Poul Creek Formation conformably overlies the Kulthieth Formation (Plafker, 1987; Miller, 1971). It is estimated to be approximately 1.9 km thick, and is composed of siltstones and organic-rich sandstones, in part glauconitic recording a marine transgression, interrupted by deposits of the Cenotaph Volcanics (Plafker, 1987). Finally, unconformably overlying the Poul Creek Formation is the Miocene to Pliocene Yakataga Formation (Miller, 1971). It is composed mainly of tillite and marine strata (Perry, Garver & Ridgway, 2009).

The Poul Creek Formation itself is broadly constrained to approximately 40–20 million years in age, from the latest Eocene to possibly early Miocene in age (Plafker, 1987; Miller, 1971). The depositional age of the unit has been further constrained to ∼24 to ∼29 Ma, or a mid to late Oligocene age, based on detrital zircon fission-track analyses of young grain-age populations (Perry, Garver & Ridgway, 2009). Using the broadest time duration for the formation (∼20 million years) and the coarse stratigraphic thickness of the sediments within it (∼2 km), a constant rate of sedimentation would suggest that the stratigraphic position of USNM 214830 at 500 m below the top of the formation would be roughly equivalent to an geochronologic age of ∼25 million years, an estimate that is consistent to the detrital zircon analyses. Overall, we propose a late Oligocene, or Chattian age for Arktocara, although we cannot exclude a Rupelian antiquity.

Diagnosis. Arktocara is a small to medium sized platanistoid odontocete (approximately 2.26 m in total length), which belongs, based on one equivocal synapomorphy, to the node-based Platanistoidea: width: width of the premaxillae >50% of the width of the rostrum at the antorbital notch (character 51[1]). More convincingly, Arktocara belongs to Platanistoidea based on its affinities to other members of the Allodelphinidae that possess unequivocal synapomorphies of the Platanistoidea (see ‘Discussion’ for further comments on the relationship of Allodelphinidae within the Platanistoidea). We also note that, for the purposes of this diagnosis, we use a broad definition of Waipatiidae that includes Otekaikea spp. (see Tanaka & Fordyce (2015a)), and Squalodelphinidae sensu Lambert, Bianucci & Urbina (2014). See ‘Discussion’ for further comments on systematics of these groups.


Etymology. The species epithet ‘yakataga’ derives from the Tlingit name for the point of land along the southeast coast of Alaska between modern day Kayak Island and Ice Bay. This point, currently called Cape Yakataga, is located directly southwest of Watson Peak and represents the southeastern boundary of a floodplain drained by the Bering Glacier. The name Yakataga was first published by Tebenkov (1852: map 7), who was a cartographer and hydrographer of the Imperial Russian Navy, as “M[ys] Yaktaga” on an 1849 map of Alaska. The geographic place name has been alternatively spelled Cape Iaktag, Cape Yakaio, Cape Yakatag, and Yokataga Reef (Orth, 1967). According to the Geographic Names Information System (GNIS, 2016), developed by USGS in cooperation with the United States Board of Geographic Names (BGN), the name “Yakataga” means “canoe road,” referring to two reefs that form a canoe passage to the shore of the village.

Figure 12: Distribution map of fossil Allodelphinidae.
Mapped of fossil localities of allodelphinids, projected on a truncated Winkel Tripel map and centered on 25°N and 170°W. Occurrences for fossil data derive from location of type and referred localities for each taxon, are listed alphabetically by region, and are represented by orange dots.

Platanistoids first appear in the fossil record in the late Oligocene, and reach peak richness in the early Miocene (Kimura & Barnes, 2016; Tanaka & Fordyce, 2015a). The oldest platanistoids with solid age constraints are the waipatiids, all found in the Oligocene-Miocene Otekaike Limestone of New Zealand (Graham et al., 2000; Benham, 1935; Fordyce, 1994; Tanaka & Fordyce, 2014; Tanaka & Fordyce, 2015a). Based on both the lithology and the presence of age-diagnostic planktic foraminifera and ostracod species, Waipatia hectori (Benham, 1935) is the oldest reported waipatiid, from the uppermost Duntroonian Stage of the Otekaike Limestone, approximately 25.2 Ma (Tanaka & Fordyce, 2015b). Arktocara is possibly very similar in age to Waipatia hectori, constrained to the Chattian Stage of the upper Oligocene in the Poul Creek Formation, approximately ∼24–29 Ma (Perry, Garver & Ridgway, 2009). Unfortunately, the lack of robust locality data for either Waipatia hectori or Arktocara makes impossible to determine which is the oldest.

Arktocara is, however, very clearly the oldest known allodelphinid, expanding the previously reported age range of Allodelphinidae by as much as 9 million years (Kimura & Barnes, 2016). Other allodelphinids span temporally from the early to middle Miocene, which largely matches the stratigraphic range of other platanistoid lineages (Fig. 11). Interestingly, Arktocara is among the oldest crown Odontoceti, reinforcing the long-standing view that the timing for the diversification for crown lineages must have occurred no later than the early Oligocene.

Lastly, Allodelphinidae appear uniquely limited, in terms of geography, to marine rocks of the North Pacific Ocean, with occurrences in Japan, Alaska, Washington State, Oregon, and California (see Fig. 12; Kimura & Barnes, 2016). Arktocara expands this geographic range to sub-Arctic latitudes. At approximately 60°N in the Yakutat City and Borough, Arktocara is the most northern platanistoid yet reported. The next most northern platanistoid reported is an incomplete and unnamed specimen from the late Chattian marine Vejle Fjord Formation in northern Denmark, approximately 56.7°N, 9.0°E (Hoch, 2000).

Alexandra T. Boersma​ and Nicholas D. Pyenson. 2016. Arktocara yakataga, a new fossil odontocete (Mammalia, Cetacea) from the Oligocene of Alaska and the antiquity of Platanistoidea.  PeerJ. 4:e2321. DOI: 10.7717/peerj.2321

New species of extinct river dolphin discovered in Smithsonian collection via @EurekAlertAAAS

[Paleontology • 2014] Lyciasalamandra antalyana gocmeni • A New Subspecies of Lyciasalamandra antalyana (Amphibia: Salamandridae) from the Lycian Coast, Turkey

Lyciasalamandra antalyana gocmeni 
Akman & Godmann, 2014

 (a) Male from the type locality, Kırkgözhan, Yağca; (b) male, (c) female, and (d) juvenile from Kızılseki. 

A new subspecies of the Lycian salamander Lyciasalamandra antalyana is described from Yağcavillage (Antalya province) and Burdur province on the Lycian Coast, Turkey. It is distinguished from the nominotypical form by its dorsal colouration, multivariate morphometrics, and mitochondrial molecular markers.

Key words. Urodela, Lyciasalamandra antalyana gocmeni ssp. n., 16SrDNA gene, Turkey.

Figure 2.  Lyciasalamandra antalyana gocmeni(a) Male from the type locality, Kırkgözhan, Yağca; (b) male, (c) female, and (d) juvenile from Kızılseki.  

Bahadir Akman and Olaf Godmann. 2014. A New Subspecies of Lyciasalamandra antalyana (Amphibia: Salamandridae) from the Lycian Coast, Turkey. Salamandra. 50(3);125-132 · 

[Botany • 2014] Hieracium attenboroughianum • A New Species of Hawkweed (Asteraceae) from the Brecon Beacons, Wales, the UK

Hieracium attenboroughianum  T.C.G.Rich

Figure 3 Pictures of Hieracium attenboroughianum.
(a) Locality on NW side of Cribyn. (b) Habitat on Old Red Sandstone mountain rocks. (c) Plant. (d) Capitulum. 

Hieracium attenboroughianum is described from the Brecon Beacons, Wales. It is a member of the H. britannicum group in Hieracium section Stelligera Zahn, related to H. britannicoides P. D. Sell but differing in cupped, dark green leaves and sparse, medium simple eglandular hairs and many glandular hairs on the involucral bracts. About 300 plants occur on Old Red Sandstone mountain ledges on Cribyn (V.c. 42). It is named after David Attenborough. It is classified under the IUCN Threat Category ‘Endangered’.

Keywords: David Attenborough, endemic, Wales

Hieracium attenboroughianum  T.C.G.Rich

 Tim Rich. 2014. Hieracium attenboroughianum (Asteraceae), A New Species of Hawkweed.  New Journal of Botany. 4(3); 172-175. DOI:  10.1179/2042349714Y.0000000051


Thursday, August 25, 2016

[Entomology • 2016] Three New Ground Wētā Species; Hemiandrus luna, H. brucei & H. nox and A Redescription of Hemiandrus maculifrons

Hemiandrus brucei 
 Taylor-Smith, Trewick & Morgan-Richards, 2016


Taxonomy lies at the heart of species conservation, yet many large New Zealand orthopterans remain undescribed. Among New Zealand’s anostostomatid wētā, Hemiandrus (ground wētā) is the most speciose genus but also the most poorly characterised and thus most in need of taxonomic and ecological work. Here we redescribe H. maculifrons and describe two new species of ground wētā previously encompassed by the specific name Hemiandrus maculifrons: Hemiandrus luna sp. nov. and H. brucei sp. nov. We also describe a morphologically similar and related species, Hemiandrus nox sp. nov.

KEYWORDS: Anostostomatidae, Hemiandrus, Orthoptera, species complex, wētā, 

B.L. Taylor-Smith, S.A. Trewick and M. Morgan-Richards. 2016.  Three New Ground Wētā Species and A Redescription of Hemiandrus maculifronsNEW ZEALAND JOURNAL OF ZOOLOGY.  DOI: 10.1080/03014223.2016.1205109

[Herpetology • 2015] Rediscovery and Redescription of Theloderma phrynoderma (Ahl, 1927) (Anura: Rhacophoridae) from Myanmar

Theloderma phrynoderma (Ahl, 1927)adult male 

 DOI: 10.1643/CH-14-130  

Theloderma is a widely distributed yet little-known genus of camouflaged tree frogs found throughout Southeast Asia. One member, T. phrynoderma, known only from the moist evergreen forest of the Karen Hills of Myanmar, is redescribed from two recently collected specimens and examination of type specimens. To date the only information available about T. phrynoderma is Boulenger’s brief 1893 description of two type specimens collected in 1888, and phylogenetic analyses to test its placement among other species of Theloderma is lacking due to an absence of specimens. In the present study, we compared two individuals collected in 2009 and 2010 from the Tanintharyi Nature Reserve to the type specimens of T. phrynoderma and proposed that they are also members of this species. We then used two mitochondrial genes (12S and 16S rRNA) and two nuclear genes (rhodopsin and tyrosinase) to infer the phylogenetic relationship of the putative T. phrynoderma to other members of Rhacophoridae, with a special emphasis on Theloderma. The recently collected individuals are of the same species within Theloderma but distinct from all other DNA sequenced congeners. The species redescription is based on a comparison of the newly found reference specimens with the lectotype and paralectotype. In addition, using a combination of morphological characters we provide a more complete diagnosis. The species is distinct from other congeners by a combination of the following characters: a mid-body size (female 44 mm SVL; male mean 41.3 mm SVL); tympanum diameter to eye diameter (70%); partial webbing between fingers; rugose skin with clumped, white-tipped calcified tubercles throughout the dorsal surface; webbing between fingers; distinct darker brown inverted V-marking between its shoulders; absence of vomerine teeth; and absence of vocal sacs.

Redescription of Theloderma phrynoderma (Ahl, 1927)
Figures 6–10; Table 3
Phrynoderma asperum Boulenger, 1893:342.
Rhacophorus phrynoderma Ahl, 1927:47.
Rhacophorus (Phrynoderma) phrynoderma Ahl, 1931:60.
Rhacophorus (Rhacophorus) leprosus phrynoderma Wolf, 1936:158.
Theloderma phrynoderma Inger, 1985:550.

Geographic distribution.—This species is known from two localities in Myanmar (Fig. 1). The lectotype and paralectotype were collected in Thao, at an elevation of 1,300–1,400 a.s.l. The collected reference specimens were collected at a lower elevation of 59–82 a.s.l. from two sites in the TNR of northern Tanintharyi Division. Although separated by approximately 550 km, the Thao collection locality and Tanintharyi collection localities lie within a contiguous tropical-subtropical moist evergreen forest ecoregion (Olson et al., 2001).

Dever, Jennifer A., Hai Nguyen and Jeffery A. Wilkinson. 2015. Rediscovery and Redescription of Theloderma phrynoderma (Ahl, 1927) (Anura: Rhacophoridae) from Myanmar. Copeia. 103 (2): 402-415. DOI: 10.1643/CH-14-130

[Herpetology • 2016] Species Boundaries and Taxonomy of the African River Frogs (Pyxicephalidae: Amietia)

 Amietia delalandii  
(Duméril & Bibron, 1841)


A molecular phylogeny of the Afrotropical anuran genus Amietia based on 323 16S sequences indicates that there are 19 species, including four not yet described. No genetic material was available for the nominal A. inyangae. We consider them to represent full species, and define them based on 16S genetic distances, as well as differences in morphology, tadpoles and advertisement call where known. An analysis based on two mitochondrial and two nuclear genes (12S, 16S, 28S and tyrosinase exon 1), from 122 samples, confirmed the phylogenetic relationships suggested by the 16S tree. We recognise and (re-) describe the following species: Amietia angolensis (Bocage, 1866), A. chapini (Noble, 1924), A. delalandii (Duméril & Bibron, 1841), A. desaegeri (Laurent, 1972), A. fuscigula (Duméril & Bibron, 1841), A. hymenopus (Boulenger, 1920), A. inyangae (Poynton, 1966), A. johnstoni (Günther, 1893), A. moyerorum sp. nov., A. nutti (Boulenger, 1896), A. poyntoni Channing & Baptista, 2013, A. ruwenzorica (Laurent, 1972), A. tenuoplicata (Pickersgill, 2007), A. vandijki (Visser & Channing, 1997), A. vertebralis (Hewitt, 1927), and A. wittei (Angel, 1924). Three further candidate species of Larson et al. (2016) await formal naming. We provisionally regard A. amieti (Laurent, 1976) as a junior synonym of A. chapini (Noble, 1924). Amietia lubrica (Pickersgill, 2007) is shown to be a junior synonym of A. nutti, while A. quecketti (Boulenger, 1895) is shown to be a junior synonym of A. delalandii (Duméril & Bibron, 1841), and A. viridireticulata (Pickersgill, 2007) is placed as a junior synonym of A. tenuoplicata (Pickersgill, 2007). On the basis of similarity of 16S sequences, we assign A. sp. 1, A. sp. 3 and A. sp. 6 of Larson et al (2016) to the nomina A. chapini (Noble, 1924), A. desaegeri (Laurent, 1972), and A. nutti (Boulenger, 1896) respectively.

Keywords: Amphibia, Africa, Amietia, molecular phylogeny, haplotypes, advertisement calls, tadpoles, new species, Amietia moyerorum sp. nov.

 A. Channing, J.M. Dehling, S. Lötters and R. Ernst. 2016.  Species Boundaries and Taxonomy of the African River Frogs (Amphibia: Pyxicephalidae: Amietia). Zootaxa.  4155(1); 1–76. 

Larson, T.R., Castro, D., Behangana, M. and Greenbaum, E. 2016. Evolutionary History of the River Frog Genus Amietia (Anura: Pyxicephalidae) reveals Extensive Diversification in Central African Highlands. Molecular Phylogenetics and Evolution. 99, 168–181.  DOI: 10.1016/j.ympev.2016.03.017

Ninda Lara Baptista. 2011. A review of Amietia angolensis (Bocage, 1866) and Amietia fuscigula (Duméril and Bibron, 1841) (Anura: Pyxicephalidae), using morphology and advertisement calls

Wednesday, August 24, 2016

[Ichthyology • 2016] Eye Lens Radiocarbon reveals Centuries of Longevity in the Greenland Shark Somniosus microcephalus

Greenland Shark Somniosus microcephalus 
photo: Nick Caloyianis DOI:  10.1126/science.aaf1703

Deep living for centuries
We tend to think of vertebrates as living about as long as we do, give or take 50 to 100 years. Marine species are likely to be very long-lived, but determining their age is particularly difficult. Nielsen et al. used the pulse of carbon-14 produced by nuclear tests in the 1950s—specifically, its incorporation into the eye during development—to determine the age of Greenland sharks. This species is large yet slow-growing. The oldest of the animals that they sampled had lived for nearly 400 years, and they conclude that the species reaches maturity at about 150 years of age.

A Greenland Shark Somniosus microcephalus off Baffin Island, Canada. 
photo: Nick Caloyianis 


The Greenland shark (Somniosus microcephalus), an iconic species of the Arctic Seas, grows slowly and reaches >500 centimeters (cm) in total length, suggesting a life span well beyond those of other vertebrates. Radiocarbon dating of eye lens nuclei from 28 female Greenland sharks (81 to 502 cm in total length) revealed a life span of at least 272 years. Only the smallest sharks (220 cm or less) showed signs of the radiocarbon bomb pulse, a time marker of the early 1960s. The age ranges of prebomb sharks (reported as midpoint and extent of the 95.4% probability range) revealed the age at sexual maturity to be at least 156 ± 22 years, and the largest animal (502 cm) to be 392 ± 120 years old. Our results show that the Greenland shark is the longest-lived vertebrate known, and they raise concerns about species conservation.

Julius Nielsen, Rasmus B. Hedeholm, Jan Heinemeier, Peter G. Bushnell, Jørgen S. Christiansen, Jesper Olsen, Christopher Bronk Ramsey, Richard W. Brill, Malene Simon, Kirstine F. Steffensen and John F. Steffensen. 2016. Eye Lens Radiocarbon reveals Centuries of Longevity in the Greenland Shark (Somniosus microcephalus). Science. 353(6300); 702-704. DOI:  10.1126/science.aaf1703

Slow Sharks Sneak Up on Sleeping Seals (and Eat Them)? via @NatGeo

[Botany • 2014] Siliquamomum alcicorne • A New Species (Zingiberaceae) from southern Vietnam

Siliquamomum alcicorne 
Škorničk. & Trần H.Đ.

Siliquamomum alcicorne (Zingiberaceae: Alpinioideae) from central Vietnam is described and illustrated here. It is compared to the other two species so far known in the genus, S. tonkinense and S. oreodoxa. A key to the three species and a map of their distribution are given. The genome size of each species has been estimated by FCM analysis. The occurrence of flexistyly in the genus Siliquamomum is reported here for the first time.

Keywords. Alpinioideae, flexistyly, flow cytometry, genome size, Siliquamomum oreodoxaSiliquamomum tonkinense, Vietnam, 2C value

Siliquamomum alcicorne Škorničk. & Trần H.Đ., sp. nov.
Similar to Siliquamomum tonkinense Baill. in its robust habit, but differs in having more leaves per leafy shoot (8–11 vs. 3–6), sessile leaf blades (vs. petiolate) and an anther which is deeply divided up to 1/3 from apex with two spathulate, green lobes (as opposed to an emarginate apex without a prominent anther crest).

TYPE: Vietnam, Kontum Province, Kon Plong Dist., Xã Hiếu, 14°38’57.7”N 108°24’57.7”E, 1223 m, 24 April 2012, J. Leong-Škorničková, Nguyễn Q.B., Trần H.Đ., E. Záveská JLS-1560 (holotype SING; isotypes E, PR, VNMN). (Fig. 1)

Key to the species of Siliquamomum
1a. Pseudostem with 3–6 leaves; petiole 2.5–9 cm long (northern Vietnam & southeastern Yunnan, China) ........................................................... S. tonkinense 
1b. Pseudostem with 8–13 leaves; petiole inconspicuous or up to 2 cm long ........... 2 

2a. Pseudostems up to 2 m long, petiole inconspicuous, anther with prominent spathulate crest-lobes above each theca (central Vietnam) ................ S. alcicorne 
2b. Pseudostems up to 0.9 m long, petiole up to 2 cm long, anther with minute sharp point above each theca (southern Vietnam) ......................................... S. oreodoxa

J. Leong-Škorničková, H.Đ. Trần, Q.B. Nguyễn and O. Šída. 2014. Siliquamomum oreodoxa (Zingiberaceae): A New Species from southern Vietnam. Gardens’ Bulletin Singapore. 66(1): 39–46.

Friday, August 19, 2016

[Ornithology / Behaviour • 2016] Evidence that Birds Sleep in Mid-Flight

Frigatebirds reaches a wingspan of over two meters. They are excellent gliders and can cover several hundred kilometers a day.
photo: B. Voirin    DOI: 10.1038/ncomms12468  

Many birds fly non-stop for days or longer, but do they sleep in flight and if so, how? It is commonly assumed that flying birds maintain environmental awareness and aerodynamic control by sleeping with only one eye closed and one cerebral hemisphere at a time. However, sleep has never been demonstrated in flying birds. Here, using electroencephalogram recordings of great frigatebirds (Fregata minor) flying over the ocean for up to 10 days, we show that they can sleep with either one hemisphere at a time or both hemispheres simultaneously. Also unexpectedly, frigatebirds sleep for only 0.69 h d−1 (7.4% of the time spent sleeping on land), indicating that ecological demands for attention usually exceed the attention afforded by sleeping unihemispherically. In addition to establishing that birds can sleep in flight, our results challenge the view that they sustain prolonged flights by obtaining normal amounts of sleep on the wing.

Figure 1: Measuring the brain state and flight mode of flying frigatebirds.
 (a) Great frigatebird Fregata minor with a head-mounted data logger for recording the electroencephalogram (EEG) from both cerebral hemispheres and head acceleration in three dimensions. A back-mounted GPS logger recorded position and altitude. Photo: B.V. (b) Overhead view of a great frigatebird skull showing (1) the position of the cranial bulge (shaded grey) overlying the hyperpallium of each hemisphere, (2) the position of the epidural electrodes (red dots, EEG; green dot, ground) and (3) the data logger (black rectangle) just posterior to the naso-frontal hinge (arrow). Scale bar is 10 mm. (c) All GPS tracks for individual birds coded with different colours. The Galapagos Islands are outlined with black lines and the study site (Genovesa) is marked by a star. Ocean depth (m) is coded with grey scale. (d) High temporal resolution (1 Hz) 10 min flight trajectory recorded with GPS from a frigatebird (see Supplementary Movie 1 for 3D visualization) showing the circling (soaring) and straight (gliding) flight modes typical of Fregatidae13 (Methods). (e) Altitude, ground speed and airspeed (computed from the GPS data in (d)), tangential and centripetal (radial) low-pass filtered acceleration, and the absolute value of total acceleration (measured by an accelerometer) for the flight in (d). 

Niels C Rattenborg, Bryson Voirin, Sebastian M. Cruz, Ryan Tisdale, Giacomo Dell’Omo, Hans-Peter Lipp, Martin Wikelski and Alexei L. Vyssotski. 2016. Evidence that Birds Sleep in Mid-Flight. Nature Communications. 7: 12468. DOI: 10.1038/ncomms12468 

First evidence of sleep in flight
Birds engage in all types of sleep in flight, but in remarkably small amounts

[Paleontology • 2015] Lohuecosuchus megadontos • New Crocodyliforms from Southwestern Europe and Definition of a Diverse Clade of European Late Cretaceous Basal Eusuchians

 Lohuecosuchus megadontos
 Narváez, Brochu, Escaso, Pérez-García and Ortega, 2015


The late Campanian-early Maastrichtian site of Lo Hueco (Cuenca, Spain) has provided a set of well-preserved crocodyliform skull and lower jaw remains, which are described here and assigned to a new basal eusuchian taxon, Lohuecosuchus megadontos gen. et sp. nov. The reevaluation of a complete skull from the synchronous site of Fox-Amphoux (Department of Var, France) allows us to define a second species of this new genus. Phylogenetic analysis places Lohuecosuchus in a clade exclusively composed by European Late Cretaceous taxa. This new clade, defined here as Allodaposuchidae, is recognized as the sister group of Hylaeochampsidae, also comprised of European Cretaceous forms. Allodaposuchidae and Hylaeochampsidae are grouped in a clade identified as the sister group of Crocodylia, the only crocodyliform lineage that reaches our days. Allodaposuchidae shows a vicariant distribution pattern in the European Late Cretaceous archipelago, with several Ibero-Armorican forms more closely related to each other than with to Romanian Allodaposuchus precedens.

Systematic Paleontology



Allodaposuchidae clade nov.
Type species: Allodaposuchus precedens 

Definition: Allodaposuchus precedens and all crocodyliforms more closely related to it than to Hylaeochampsa vectiana, Shamosuchus djadochtaensis, Borealosuchus sternbergii, Planocrania datangensis, Alligator mississippiensis, Crocodylus niloticus, or Gavialis gangeticus.

Included species: Allodaposuchus precedens; Massaliasuchus affuvelensis; Musturzabalsuchus buffetauti; Arenysuchus gascabadiolorum; Allodaposuchus subjuniperus; Allodaposuchus palustris; Allodaposuchus hulki, Lohuecosuchus megadontos sp. nov.; Lohuecosuchus mechinorum sp. nov.


Iván Narváez, Christopher A. Brochu, Fernando Escaso, Adán Pérez-García and Francisco Ortega. 2015. New Crocodyliforms from Southwestern Europe and Definition of a Diverse Clade of European Late Cretaceous Basal Eusuchians. PLoS ONE. 10(11): e0140679. DOI: 10.1371/journal.pone.0140679

 Lohuecosuchus megadontos 
Narváez, Brochu, Escaso, Pérez-García and Ortega, 2015

[Ichthyology • 2008] Three New Pygmy Seahorse Species (Syngnathidae: Hippocampus) from Indonesia; Hippocampus pontohi, H. severnsi & satomiae

FIGURE 4. Live specimens of new species of pygmy seahorses from Indonesia.
AHippocampus pontohi: Bunaken, Sulawesi, M. Boyer; Bunaken, Sulawesi, M. Aw; Raja Ampat, West Papua, L. Tackett. BHippocampus severnsi: Bunaken, Sulawesi, S. Wong & T. Uno; Bunaken, Sulawesi, M. Severns (type specimens); Raja Ampat, West Papua, L. Tackett. CHippocampus satomiae: Derawan Kalimantan, S. Wong & T. Uno; Derawan, Kalimantan, J–S. Chen; Derawan, Indonesia, S. Onishi (type specimen).  

Three new species of pygmy seahorse are described from Indonesia: Hippocampus pontohi and H. severnsi from Bunaken Island, off Sulawesi, and H. satomiae from Derawan Island, off Kalimantan. They are considered to be closely related to each other and to Hippocampus colemani. All three species are morphologically distinguished from the larger species of seahorses by the following combination of characters: 12 trunk rings, low number of tail rings (26–29), the placement of brooded young within the trunk region of males, and extremely small size (<15 mm HT, <17 mm SL). They can be separated from the previously described species of pygmy seahorses (H. bargibantiH. deniseH. colemani and H. minotaur) based on meristics, proportions, colour and body ornamentation. All three new species have a single gill opening as does H. colemani. Hippocampus pontohi and H. severnsi also share distinctive fleshy appendages with H. colemani but can be separated from the latter based on their body shape, raised angular coronet, larger orbit diameter, narrower trunk, fewer tail rings, smaller overall size and in the case of H. severnsi also colour. Diagnostic features of H. satomiae include 9 pectoral fin rays, 13 dorsal fin rays, spinous exterior, and distinct raised coronet with laterally expanded anterior and posterior flanges.

Key words: Hippocampus pontohiHippocampus severnsiHippocampus satomiae, new species, taxonomy, Indo-Pacific, marine

FIGURE 4. Live specimens of new species of pygmy seahorses from Indonesia.
AHippocampus pontohi: Bunaken, Sulawesi, M. Boyer; Bunaken, Sulawesi, M. Aw; Raja Ampat, West Papua, L. Tackett. BHippocampus severnsi: Bunaken, Sulawesi, S. Wong & T. Uno; Bunaken, Sulawesi, M. Severns (type specimens); Raja Ampat, West Papua, L. Tackett. CHippocampus satomiae: Derawan Kalimantan, S. Wong & T. Uno; Derawan, Kalimantan, J–S. Chen; Derawan, Indonesia, S. Onishi (type specimen). 

Hippocampus pontohi sp. nov.  

Etymology. This species is named in honour of Hence Pontoh, the Indonesian dive guide who first brought these pygmy seahorses to our attention. 

Distribution and ecology. Hippocampus pontohi has been observed on the coralline algae Halimeda, as well as on the hydroid Aglaephenia cupressina (Müller and Severns, pers. comm.). Severns noted it particularly in areas where Halimeda is growing on reef walls. It has been recorded at a number of areas in Indonesia (Bunaken, Cape Sri, Sorong, Wakatobi, Lembeh Straits), at depths of between 11–25 m particularly on vertical walls or in rock fissures (Müller, pers. comm.). See figure 5A for map. 
Hippocampus pontohi is commonly found in pairs and, like H. denise, is relatively active (Müller, pers. comm.). Two of the specimens examined were pregnant (MZB 13593 and MZB 13596) and each contained approximately 11 embryos. Both were collected in July. 

Hippocampus severnsi sp. nov.

Etymology. Hippocampus severnsi is named in honour of Mike Severns who, with Hence Pontoh, collected the first specimens. 

Distribution and ecology. Hippocampus severnsi is known from Indonesia (Bunaken, Wakatobi, Raja Ampat Islands, Kawe Island), Japan (Ryukyu Islands), Papua New Guinea (Milne Bay, Madang), Solomon Islands (Mborokua) and Fiji at depths of 8–20 m. See figure 5B for map. It has been observed both during the day and the night but is apparently more active in the morning and late afternoon when it is not in direct sunlight (Müller, pers. comm.). In Indonesia it has been recorded in association with a yellow coloured bryozoan, Catenicella sp., on different kinds of hydrozoans including Lytocarpus phoeniceaAntennellopsis integerrima and Halicordyle disticha (Müller, perscomm.) as well as in sheltered spots on a reef wall in association with Halimeda (Brett, perscomm.). It is also recorded from fissures on current–swept walls where it will tend to occur on the side of the fissure that faces away from the current, but in all cases where there is some upward current (Müller, pers. comm.) and has been seen swimming over a fungiid coral (Hardt, pers. comm.). In Papua New Guinea it has been observed in a healthy reef passage with a regular current of up to two knots on a gorgonian of the genus Muricella at 12 m depth (Halstead, pers. comm.) and in Fiji it was found on gorgonian species, possibly Menella sp.? (Tackett, pers. comm.) 
The holotype of H. severnsi, collected in June, had approximately 11 embryos within its pouch

Hippocampus satomiae

Etymology. This species is named in honour of Miss Satomi Onishi, the dive guide who collected the type specimens. 

Distribution and ecology. Hippocampus satomiae is known from scattered localities in Indonesia, including Derawan (type locality), and Lembeh Strait (northern Sulawesi), as well as northern Borneo, Malaysia. See figure 5C for map. It congregates at night in groups of 3–5 individuals on small seafans, at depths of 15–20 m depth on the bottom below reef overhangs. Photographed individuals (in Boyer, 2007) from the Togean Islands, Indonesia on a species of Nepthea Auduoin, 1826 on the reef front in water as shallow as 5 m are tentatively identified as H. satomiae.
 During the day H. satomiae are difficult to find, even in areas where they are known to occur. At dawn individuals become active. Birth has been observed on a number of occasions and also photographed. At birth, the young are jet–black, about 3 mm in height and shaped similarly to the adults. They settle on the bottom near to their place of birth (Onishi, pers. comm.). 
The holotype, collected in October, was pregnant and carrying approximately eight young.  

Sara A. Lourie and Rudie H. Kuiter. 2008. Three New Pygmy Seahorse Species from Indonesia (Teleostei: Syngnathidae: Hippocampus). Zootaxa. 1963: 54–68.