[Herpetology • 2019] Diversification of Shrub Frogs (Rhacophoridae, Pseudophilautus) in Sri Lanka – Timing and Geographic Context

in Meegaskumbura, Senevirathne, Manamendra-Arachchi, et al., 2019. 

  DOI: 10.1016/j.ympev.2018.11.004 

Highlights

• Pseudophilautus diversification, begins during Oligocene (31 MYA)

• A stately pace of lineage accumulation despite orogeny and climate change.

• Assemblages in most regions comprise of species arising from diverse clades.

• MRCA of a back-migrating clade to India (8.8 MYA), reconstructs as a lowland form.

 • Island’s mountains serve as species pumps and refuges for Pseudophilautus evolution.

Abstract

Pseudophilautus comprises an endemic diversification predominantly associated with the wet tropical regions of Sri Lanka that provides an opportunity to examine the effects of geography and historical climate change on diversification. Using a time-calibrated multi-gene phylogeny, we analyze the tempo of diversification in the context of past climate and geography to identify historical drivers of current patterns of diversity and distribution. Molecular dating suggests that the diversification was seeded by migration across a land-bridge connection from India during a period of climatic cooling and drying, the Oi-1 glacial maximum around the Eocene-Oligocene boundary. Lineage-through-time plots suggest a gradual and constant rate of diversification, beginning in the Oligocene and extending through the late Miocene and early Pliocene with a slight burst in the Pleistocene. There is no indication of an early-burst phase of diversification characteristic of many adaptive radiations, nor were there bursts of diversification associated with favorable climate shifts such as the intensification of monsoons. However, a late Miocene (8.8 MYA) back-migration to India occurred following the establishment of the monsoon. The back migration, however, did not trigger a diversification in India similar to that manifest in Sri Lanka, likely due to occupation of available habitat, and consequent lack of ecological opportunity, by the earlier radiation of a sister lineage of frogs (Raorchestes) with similar ecology. Phylogenetic area reconstructions show a pattern of sister species distributed across adjacent mountain ranges or from different parts of large montane regions, highlighting the importance of isolation and allopatric speciation. Hence, local species communities are composed of species from disparate clades that, in most cases, have been assembled through migration rather than in situ speciation. Lowland lineages are derived from montane lineages. Thus, the hills of Sri Lanka acted as species pumps as well as refuges throughout the 31 million years of evolution, highlighting the importance of tropical montane regions for both the generation and maintenance of biodiversity.

Keywords: Ancestral-area reconstruction, Biogeography, Ecological opportunity, Diversification, Molecular dating, Speciation

 Madhava Meegaskumbura, Gayani Senevirathne, Kelum Manamendra-Arachchi, Rohan Pethiyagoda, James Hanken and Christopher J. Schneider. 2019. Diversification of Shrub Frogs (Rhacophoridae, Pseudophilautus) in Sri Lanka – Timing and Geographic context. Molecular Phylogenetics and Evolution. In Press. DOI: 10.1016/j.ympev.2018.11.004

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[Ornithology • 2018] Complete Species-level Phylogeny of the Leaf Warbler (Aves: Phylloscopidae) Radiation

Phylogeny of Phylloscopidae 

in Alström, Rheindt, Zhang, Zhao, Wang, et al., 2018. 

DOI: 10.1016/j.ympev.2018.03.031 

twitter.com/AlstromPer 

Highlights

• Complete species-level phylogeny for Seicercus and Phylloscopus.

• Time calibrated phylogeny.

• Taxonomic revision of Phylloscopidae.

Abstract

The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8–13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3–0.8 mya) to 6.1 mya (4.8–7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment, and we argue against proliferation of taxonomic names, and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications.

We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.

Keywords: Species tree, Concatenation, Taxonomic revision

Phylogeny of Phylloscopidae based on the mitochondrial cytochrome b and nuclear ODC, myoglobin and GAPDH introns inferred by ∗BEAST. Traditional Seicercus species are highlighted in red. 

Photo by Craig Brelsford (14), James Eaton (2, 10, 18, 19), Göran Ekström (9, 15, 16, 22), Jocko Hammar (6), Jonathan Martinez (5, 7, 8, 11, 20), Yann Muzika (1), Frédéric Pelsy (12), Megan & Chris Perkins (3), Nick Robinson (4, 13, 17, 21). 

DOI: 10.1016/j.ympev.2018.03.031 

 twitter.com/AlstromPer 

  

Conclusions:

 The generally well resolved and well supported time calibrated phylogeny is a major step forward compared to earlier studies based on a smaller number of species and loci. This can provide a basis for future studies of other aspects of the evolution of this ecologically important group of birds.

Per Alström, Frank E. Rheindt, Ruiying Zhang, Min Zhao, Jing Wang, Xiaojia Zhu Chyi Yin Gwee, Yan Hao, Jan Ohlson, Chenxi Jia, Dewi M. Prawiradilaga, Per G. P. Ericson, Fumin Lei and Urban Olsson. 2018. Complete Species-level Phylogeny of the Leaf Warbler (Aves: Phylloscopidae) Radiation. Molecular Phylogenetics and Evolution.  126; 141-152. DOI: 10.1016/j.ympev.2018.03.031 

 twitter.com/AlstromPer/status/1055172495404384256

[Mollusca • 2018] Sacoproteus gen. n. • Cryptic Speciation yields Remarkable Mimics: A New Genus of Sea Slugs that masquerade as Toxic Algae (Caulerpa spp.)

Sacoproteus smaragdinus  (Baba 1949), 

Krug, Wong, Medina, Gosliner & Valdés, 2018

 DOI: 10.1111/zsc.12310 

Abstract

“Cryptic” can refer to species that match their background through camouflage or disruptive colouration, or in taxonomy to externally similar but unrecognized congeners. In adaptive resemblance, organisms resemble parts of a larger host animal or plant on which the mimic is highly cryptic. Mimetic lineages that radiate onto superficially similar hosts may contain cryptic species in both senses: taxa that are difficult to detect, and challenging for taxonomists to distinguish. Here, we describe a new genus and four species of herbivorous sea slugs (Gastropoda, Heterobranchia, Sacoglossa), including remarkable mimics of toxic green algae (Caulerpa spp.) on which the slugs feed. The long‐recognized Stiliger smaragdinus Baba 1949 is highly mimetic of “sea grapes” (Caulerpa racemosa‐lentillifera), but phylogenetic analyses of four genes indicated Stiliger was polyphyletic: the name‐bearing species grouped within Placida, whereas Caulerpa‐mimetic lineages were phylogenetically distinct. We erect the genus Sacoproteus gen. n. for S. smaragdinus (Baba 1949), and describe four new species: Sacoproteus nishae sp. n. from the Indo‐Pacific, which mimics Caulerpa chemnitzia; Sacoproteus yhiae sp. n. and Sacoproteus browni sp. n. from southern Australia, which mimic Caulerpa cactoides and Caulerpa gemminata; and Sacoproteus thomasleei sp. n., a non‐mimetic west Pacific species that shared key features. Stiliger s.s. and Placida species show crypsis and aposematism but not host mimicry, although Stiliger spp. feeding on undefended algae may be Batesian mimics. Investigating the ecology and biogeography of Sacoproteus gen. n. will yield insight into how selection generates such extraordinary examples of adaptive resemblance in the marine realm.

KEYWORDS: aposematism, coevolution, cryptic species, heterobranch, mimicry, phylogenetic systematics

FIGURE 1 Photographs and illustrations of live specimens in the Stiliger smaragdinus complex.
 (a) Sacoproteus smaragdinus gen. n. (bottom arrow indicates white rhinophores, body of slug above) and S. nishae sp. n. (top arrow indicates pale green rhinophores, body of slug below) from Malaysia, cryptic on the alga Caulerpa lentillifera. (b) Live S. smaragdinus from Malaysia showing diagnostic stripes on head and pointed ceratal tips. (c) Specimen of S. smaragdinus from the Philippines (CASIZ 199257). (d) Original illustration accompanying description of S. smaragdinus (Baba, 1949). (e) Close‐up of specimen of S. nishae sp. n. from Malaysia, showing mushroom‐shaped cerata and distinctive head markings. (f) Holotype of S. yhiae sp. n. (AM 469592) from New South Wales, Australia. (g) Caulerpa cactoides, a preferred host alga for S. yhiae sp. n., from Bunurong Marine National Park, Victoria, Australia; photo credit: Julian Finn, Museums Victoria. (h) Holotype of S. thomasleei sp. n. (LACM 3496) from Guam; actual body length of specimen = 3 mm

 

 From their torpedo-like shape to their white tips, the bulbs on Sacoproteus smaragdinus's back look just like the sea grapes of Caulerpa lentillifera.

Sacoproteus gen. n.

We erect the genus Sacoproteus gen. n. for S. smaragdinus (Baba 1949), 

four new species: 

Sacoproteus nishae sp. n. from the Indo‐Pacific, which mimics Caulerpa chemnitzia

 Sacoproteus yhiae sp. n. and Sacoproteus browni sp. n. from southern Australia, which mimic Caulerpa cactoides and Caulerpa gemminata

Sacoproteus thomasleei sp. n., a non‐mimetic west Pacific species that shared key features. 

Sacoproteus nishae's mushroom-shaped bulbs let it blend in perfectly with the algae Caulerpa chemnitzia.  

Patrick J. Krug, Nur Leena W. S. Wong, Melanie R. Medina, Terrence M. Gosliner and Ángel A. Valdés. 2018. Cryptic Speciation yields Remarkable Mimics: A New Genus of Sea Slugs that Masquerade as Toxic Algae (Caulerpa spp.). Zoologica Scripta.  DOI: 10.1111/zsc.12310

Stunning new sea slug species look just like seaweed  

on.natgeo.com/2QUin8y via @NatGeo

 twitter.com/fleliaer/status/1044148506800398341

    

[Entomology • 2018] Cryptic Speciation associated with Geographic and Ecological Divergence in Two Amazonian Heliconius Butterflies

Rosser, Freitas, Huertas, Joron, Mérot, et al., 2018. 

DOI: 10.1093/zoolinnean/zly046 

Abstract

The evolution of reproductive isolation via a switch in mimetic wing coloration has become the paradigm for speciation in aposematic Heliconius butterflies. Here, we provide a counterexample to this, by documenting two cryptic species within the taxon formerly considered Heliconius demeter Staudinger, 1897. Amplified fragment length polymorphisms identify two sympatric genotypic clusters in northern Peru, corresponding to subspecies Heliconius demeter ucayalensis H. Holzinger & R. Holzinger, 1975 and Heliconius demeter joroni ssp. nov. These subspecies are reciprocally monophyletic for the mitochondrial genes COI and COII and the nuclear gene Ef1α, and exhibit marked differences in larval morphology and host plant use. COI sequences from 13 of the 15 currently recognized subspecies show that mtDNA differences are reflected across the range of H. demeter, with a deep phylogenetic split between the southern and northern Amazonian races. As such, our data suggest vicariant speciation driven by disruptive selection for larval performance on different host plants. We raise Heliconius demeter eratosignis (Joicey & Talbot, 1925) to Heliconius eratosignis based on nomenclatural priority, a species also comprising H. eratosignis ucayalensis comb. nov. and three other southern Amazonian races. Heliconius demeter joroni spp. nov. remains within H. demeter s.s., along with northern Amazonian and Guianan subspecies.

Keywords: butterflies, cryptic species, genotypic clusters, host plant shift, integrative taxonomy, mimicry, vicariant speciation

Figure 1. Distribution of races of H. demeter and H. eratosignis. Photos of type specimens are all males, except for H. e. ucayalensis. The inset shows fine-scale sympatry between H. d. joroni ssp. nov. and H. e. ucayalensis in the Tarapoto area of Peru. Heliconius demeter beebei Turner, 1966 and H. d. terrasanta appear to conform to the type specimens only around the type localities (in Terrasanta, Pará, and in Guyana). Between these, most populations appear to be either polymorphic or exhibit intermediate phenotypes (mixed square and cross symbols in the map). Heliconius demeter ssp. nov. refers to three males in the FLMNH recognized by W. Neukirchen as distinct from other described subspecies. These individuals may prove to have affinities to H. demeter titan. Distribution of races of H. demeter and H. eratosignis. Photos of type specimens are all males, except for H. e. ucayalensis. The inset shows fine-scale sympatry between H. d. joroni ssp. nov. and H. e. ucayalensis in the Tarapoto area of Peru. Heliconius demeter beebei Turner, 1966 and H. d. terrasanta appear to conform to the type specimens only around the type localities (in Terrasanta, Pará, and in Guyana). Between these, most populations appear to be either polymorphic or exhibit intermediate phenotypes (mixed square and cross symbols in the map). Heliconius demeter ssp. nov. refers to three males in the FLMNH recognized by W. Neukirchen as distinct from other described subspecies. These individuals may prove to have affinities to H. demeter titan.

Figure 3. Holotype ♂ of Heliconius demeter joroni Lamas and Rosser ssp. nov.
Upper photo: dorsal, lower photo: ventral. Scale bar = 10 mm. Holotype ♂ of Heliconius demeter joroni Lamas and Rosser ssp. nov. Upper photo: dorsal, lower photo: ventral.

Scale bar = 10 mm.

Heliconius demeter joroni Lamas & Rosser ssp. nov.  
Heliconius demeter [ssp. nov.] Lamas, MS: Lamas, 2004: 268. Lamas & Jiggins, 2017: 224.

Diagnosis: Heliconius demeter joroni ssp. nov. is similar to H. demeter demeter, but differs from Staudinger’s syntypes of H. demeter from Iquitos, Loreto, Peru (now in the MNB) in having a much narrower yellow postmedian band on the dorsal forewing. It is known only from the Cordillera Escalera, near Tarapoto, Peru (Fig. 1), where its co-mimics include Heliconius eratosignis ucayalensis, Heliconius elevatus pseudocupidineus Neustetter, 1931, Heliconius aoede cupidineus Stichel, 1906 and Eueides tales michaeli Zikán, 1937, among others. Males are easily distinguishable from all sympatric taxa through the fused rays on the hindwing dorsum and the yellow costal streak on the forewing underside. Females may be distinguished from co-mimics through the configuration of the rays (which radiate from the cell), small size, length of the antennae (longer than the forewing discal cell) and the presence of the forewing underside yellow costal streak. Both sexes usually exhibit a single row of white submarginal dots along the anal margin of the ventral hindwing, which can be used to help separate the females from H. erato emma and E. tales michaeli. This character can be faint or even missing in H. demeter joroni ssp. nov. and occasionally present in H. erato emma. However, the latter is confined to the Amazonian lowlands adjacent to the Cordillera Escalera, and at present there is no evidence to suggest that they regularly co-occur, barring occasional migrants.


Etymology: The subspecies name (a masculine noun in the genitive case) recognizes the contribution of the French evolutionary biologist Dr Mathieu Joron to the knowledge of the mimetic butterfly fauna of San Martín, Peru. Dr Joron is presently a Senior Scientist at the Centre d’Ecologie Fonctionnelle et Evolutive in Montpellier. He began studying the butterflies of San Martín during his PhD and has continued to do so throughout his career, with a particular focus on Heliconius numata.

Geographic distribution: Subspecies of H. demeter and H. eratosignis are mapped in Fig. 1, with photos of a type specimen of each race. Races of H. demeter occupy the Guianas and much of the Amazon basin. H. eratosignis races occur in the west and south of the Amazon basin. In Tarapoto, the two species fly together at a number of sites in the Cordillera Escalera. Only H. eratosignis has been recorded from the adjacent Amazonian lowlands, despite considerable sampling in the area. Museum data and observations by Keith Brown (1979) suggest that the two overlap (at least broadly) in the extreme south of Pará and northern Mato Grosso, in Brazil. There may well also be a contact zone on the Juruá River, between Porto Walter and Eirunepé, as both H. demeter demeter and H. eratosignis tambopata are known to occur there. However, the exact position of contact in this very large area is unclear. In data published by Brown (1979) two additional contact zones are indicated, at Pucallpa, Peru and near Cobija on the Brazilian/Bolivian border. We were unable to locate the relevant specimens in museum collections; however, we consider these points unreliable and excluded them from the distribution map in Fig. 1. The first is probably a generalized locality, with the specimens potentially coming from a large area of northern Peru. The second is likely explained through the co-occurrence of both H. eratosignis ulysses and H. eratosignis tambopata, as the latter was not described at the time (Lamas, 1985).

Neil Rosser, André V. L. Freitas, Blanca Huertas, Mathieu Joron, Gerardo Lamas Claire Mérot, Fraser Simpson, Keith R. Willmott, James Mallet and Kanchon K. Dasmahapatra. 2018. Cryptic Speciation associated with Geographic and Ecological Divergence in Two Amazonian Heliconius Butterflies. Zoological Journal of the Linnean Society. zly046.  DOI: 10.1093/zoolinnean/zly046

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[Herpetology • 2018] Speciation in the Mountains and Dispersal by Rivers: Molecular Phylogeny of Eulamprus Water Skinks and the Biogeography of Eastern Australia

Top left is a topographic map of the Australian continent (red = high, green = low, major drainage lines = white). 

Bottom left map shows finer‐scale drainage lines (Global Map Australia 1M 2001, Geoscience Australia) overlain on to a digital elevation model image (Shuttle Radar Topography Mission) where light grey equates to areas of high elevation, and dark grey equates to areas of low elevation. 

Right panel shows the distribution of the five Eulamprus species; E. quoyii (A, purple), E. kosciuskoi and E. leuraensis (B, yellow and red, respectively), E. heatwolei (C, green) and E. tympanum (D, pink). 

(Photos: Stephen Zozaya & Stewart Macdonald).

in Pepperm, Sumner, Brennan, et al., 2018.

  DOI: 10.1111/jbi.13385  

 twitter.com/ian_g_brennan   twitter.com/JBiogeography

Abstract

Aim: 

To develop a robust phylogeny for the iconic Australian water skinks (Eulamprus) and to explore the influence of landscape evolution of eastern Australia on phylogeographic patterns.

Location: Eastern and south‐eastern Australia.

Methods: 

We used Sanger methods to sequence a mitochondrial DNA (mtDNA) locus for 386 individuals across the five Eulamprus species to elucidate phylogeographic structure. We also sequenced a second mtDNA locus and four nuclear DNA (nDNA) loci for a subset of individuals to help inform our sampling strategy for next‐generation sequencing. Finally, we generated an anchored hybrid enrichment (AHE) approach to sequence 378 loci for 25 individuals representing the major lineages identified in our Sanger dataset. These data were used to resolve the phylogenetic relationships among the species using coalescent‐based species tree inference in *BEAST and ASTRAL.

Results: 

The relationships between Eulamprus species were resolved with a high level of confidence using our AHE dataset. In addition, our extensive mtDNA sampling revealed substantial phylogeographic structure in all species, with the exception of the geographically highly restricted E. leuraensis. Ratios of patristic distances (mtDNA/nDNA) indicate on average a 30‐fold greater distance as estimated using the mtDNA locus ND4.

Main conclusions: 

The major divergences between lineages strongly support previously identified biogeographic barriers in eastern Australia based on studies of other taxa. These breaks appear to correlate with regions where the Great Escarpment is absent or obscure, suggesting topographic lowlands and the accompanying dry woodlands are a major barrier to dispersal for water skinks. While some river corridors, such as the Hunter Valley, were likely historically dry enough to inhibit the movement of Eulamprus populations, our data indicate that others, such as the Murray and Darling Rivers, are able to facilitate extensive gene flow through the vast arid and semi‐arid lowlands of New South Wales and South Australia. Comparing the patristic distances between the mitochondrial and AHE datasets highlights the continued value in analysing both types of data.

Keywords: anchored hybrid enrichment, Eastern Australia, gene flow, great dividing range, Murray–Darling Basin, Newer Volcanics Province

Figure 1: Phylogenomic analyses provide consistent support of interspecific relationships among Eulamprus water skinks, regardless of reconstruction method. Lizard images to the left depict the relative size and appearance of each species. The first and third trees in this figure were constructed using anchored phylogenomics data (nuclear exons—nDNA), resulting in identical topologies between the full (378) and filtered (281) datasets. On these two trees (nDNA starBEAST and nDNA ASTRAL), nodes labelled with a white circle denote fully supported relationships (posterior probability = 1, bootstrap = 100), with all other nodes labelled according to estimated support. Note terminal branch lengths in ASTRAL analysis are fixed, and not to scale. The middle phylogeny has been reconstructed using the mitochondrial locus ND4 (mtDNA), with nodes labelled by a red circle constrained to match the nuclear species tree topology. Intraspecific relationships of the mtDNA tree remained unconstrained, and are used to illustrate the sampling depth and relative diversity of each species. Labels on the far right of this figure match the nDNA ASTRAL tree, run on phased haplotype data, where each taxon is represented by two terminal tips representing the phased alleles. Sampling data for each individual can be found in Table S1. Colours designated for each species correspond to sampling maps in Figure 2, and intraspecific mtDNA phylogenies in supplemental materials (Figures S1–S4)

Figure 2: Top left is a topographic map of the Australian continent (red = high, green = low, major drainage lines = white). Bottom left map shows finer‐scale drainage lines (Global Map Australia 1M 2001, Geoscience Australia) overlain on to a digital elevation model image (Shuttle Radar Topography Mission) where light grey equates to areas of high elevation, and dark grey equates to areas of low elevation. Thick dark grey lines indicate biogeographic barriers mentioned in the text. Stippled blue lines indicate the major rivers; Darling River (DR), Lachlan River (LR), Murrumbidgee River (MBR) and Murray River (MR). Coloured symbols represent sampling localities for two clades that use rivers to facilitate long‐distance gene flow. Purple triangles indicate one of the E. quoyii clades, while green circles representing our sample localities for one of the E. heatwolei clades. State boundaries are shown by thin grey lines. QLD = Queensland, SA = South Australia, NSW = New South Wales, ACT = Australian Capital Territory, VIC = Victoria.

Right panel shows the distribution of the five Eulamprus species; E. quoyii (A, purple), E. kosciuskoi and E. leuraensis (B, yellow and red, respectively), E. heatwolei (C, green) and E. tympanum (D, pink). Different coloured shapes on each map refer to major clades within each species, whereas small black + symbols refer to museum locality records. Relevant biogeographic barriers from the larger map to the left have been overlain 

(Photo credit: Stephen Zozaya & Stewart Macdonald).

Mitzy Pepperm, Joanna Sumner, Ian G. Brennan, Kate Hodges, Alan R. Lemmon, Emily Moriarty Lemmon, Garry Peterson, Daniel L. Rabosky, Lin Schwarzkopf, Ian A. W. Scott, Glenn Shea and J. Scott Keogh. 2018. Speciation in the Mountains and Dispersal by Rivers: Molecular Phylogeny of Eulamprus Water Skinks and the Biogeography of Eastern Australia. Journal of Biogeography. DOI: 10.1111/jbi.13385

 twitter.com/ian_g_brennan/status/1013921452133789697 

 twitter.com/JBiogeography/status/1014080681733967872

[Ornithology • 2018] Comprehensive Molecular Phylogeny of Barn Owls and Relatives (Family: Tytonidae), and Their Six Major Pleistocene Radiations

in Uva, Päckert, Cibois, et al., 2018. 

DOI: 10.1016/j.ympev.2018.03.013 

Highlights

• Tytonidae originated in the Oligocene (ca. 28 mya) of Australasia.

• Tytonidae underwent six trans-continental radiations in the Pleistocene.

• Split of Tyto alba into three species (T. alba, T. furcata, T. javanica) is supported.

• T. rosenbergii and T. nigrobrunnea are subspecies of T. javanica; T. sororcula and T. manusi are subspecies of T. novaehollandiae.

• Grass owls and sooty owls are a single species each (T. capensis and T. tenebricosa).

Abstract

The owl family Tytonidae comprises two genera: Phodilus, limited to the forests of central Africa and South-East Asia, and the ubiquitous Tyto. The genus Tyto is majorly represented by the cosmopolitan Common Barn Owl group, with more than 30 subspecies worldwide. Discrete differences in body size and plumage colouration have led to the classification of this family into many species and subspecies, but the taxonomic status and phylogenetic relationships between taxa remain unclear, and in some groups controversial. Although several previous studies attempted to resolve this problem, they have been limited in their taxonomic and geographical coverage, or have relied on restricted molecular evidence and low sample sizes. Based on the most comprehensive sampling to date (16 out of 17 Tyto species, and one out of three Phodilus species), a multi-locus approach using seven mitochondrial and two nuclear markers, and taking advantage of field data and museum collections available worldwide, our main questions in this study were: (1) what are the phylogenetic relationships and classification status of the whole family; (2) when and where did the most important speciation events occur? We confirm that the Common Barn Owl, Tyto alba is divided into three main evolutionary units: the American Barn Owl, T. furcata; the Western Barn Owl, T. alba; and the Eastern Barn Owl, T. javanica, and suggest a Late Miocene (ca. 6 mya) Australasian and African origin of the group. Our results are supported by fossil age information, given that the most recent common ancestor between the Tytonidae genera Phodilus and Tyto was probably from the Oligocene (ca. 28 mya) of Australasia. We finally reveal six major Pleistocene radiations of Tyto, all resulting in wide-range distributions.

Keywords: Bird, Strigiformes, Molecular phylogenetics, Taxonomical classifications

  Vera Uva, Martin Päckert, Alice Cibois, Luca Fumagalli and Alexandre Roulin. 2018. Comprehensive Molecular Phylogeny of Barn Owls and Relatives (Family: Tytonidae), and Their Six Major Pleistocene Radiations. Molecular Phylogenetics and Evolution.  125; 127-137.  DOI: 10.1016/j.ympev.2018.03.013

[Herpetology • 2018] Species Delimitation in the Gehyra nana (Squamata: Gekkonidae) Complex: Cryptic and Divergent Morphological Evolution in the Australian Monsoonal Tropics, with the Description of Four New Species

(B) G. nana  Storr, 1978

(upper & C) G. paranana & (D) G. pseudopunctata 

Doughty, Bourke, Tedeschi, Pratt, Oliver, Palmer & Moritz, 2018. 

  DOI:  10.11646/zootaxa.4403.2.1

 twitter.com/AusHerpetology  twitter.com/SVMahony

Abstract

Recent advances in molecular genetic techniques and increased fine scale sampling in the Australian Monsoonal Tropics (AMT) have provided new impetus to reassess species boundaries in the Gehyra nana species complex, a clade of small-bodied, saxicolous geckos which are widely distributed across northern Australia. A recent phylogenomic analysis revealed eight deeply divergent lineages that occur as a series of overlapping distributions across the AMT and which, as a whole, are paraphyletic with four previously described species. Several of these lineages currently included in G. nana are phenotypically distinct, while others are highly conservative morphologically. Here we use an integrated approach to explore species delimitation in this complex. We redefine G. nana as a widespread taxon with complex genetic structure across the Kimberley of Western Australia and Top End of the Northern Territory, including a lineage with mtDNA introgressed from the larger-bodied G. multiporosa. We describe four new species with more restricted distributions within the G. nana complex. The new species are phylogenetically divergent and morphologically diagnosable, and include the relatively cryptic G. paranana sp. nov. from the western Northern Territory, the large-bodied G. pseudopunctata sp. nov. from the southern Kimberley ranges, G. granulum sp. nov., a small-bodied form with granules on the proximal lamellae from the north-west and southern Kimberley ranges and the small-bodied G. pluraporosa sp. nov. restricted to the northern Kimberley. Our revision largely stabilises the taxonomy of the G. nana complex, although further analyses of species limits among the remaining mostly parapatric lineages of G. nana sensu stricto are warranted.

Keywords: Reptilia, Australian Monsoonal Tropics, cryptic speciation, gecko, Gehyra granulum sp. nov., Gehyra multiporosa, Gehyra paranana sp. nov., Gehyra pluraporosa sp. nov., Gehyra pseudopunctata sp. nov., Kimberley, lizard, Northern Territory, Top End, Western Australia

FIGURE 5. Photos in life of the species described herein.
 A) Gehyra nana (lineage nana2) (NTM R37597) from Bradshaw Field Training Area, NT (S. Mahony), B) G. nana (nanamulti) (WAM R174051) from Drysdale River National Park, WA (R.J. Ellis), C) G. paranana sp. nov. (NTM R37601) from Bradshaw Field Training Area, NT (S. Mahony), D) G. pseudopunctata sp. nov. (not collected) from near Halls Ck, WA (S. Zozaya),  

Gehyra paranana 

photo: Stephen Mahony ‏

twitter.com/SVMahony

Paul Doughty, Gayleen Bourke, Leonardo G. Tedeschi, Renae C. Pratt, Paul M. Oliver, Russell A. Palmer and Craig Moritz. 2018. Species Delimitation in the Gehyra nana (Squamata: Gekkonidae) Complex: Cryptic and Divergent Morphological Evolution in the Australian Monsoonal Tropics, with the Description of Four New Species. Zootaxa. 4403(2); 201–244. DOI:  10.11646/zootaxa.4403.2.1

 twitter.com/AusHerpetology/status/981424755130732545

 twitter.com/SVMahony/status/981430853933903873

[Herpetology • 2017] Arboreality Constrains Morphological Evolution but Not Species Diversification in Vipers

Stejneger's Pitviper (Trimeresurus stejnegeri) 

 Alencar, Martins, Burin & Quental, 2017

    DOI: 10.1098/rspb.2017.1775 

Abstract

An increase in ecological opportunities, either through changes in the environment or acquisition of new traits, is frequently associated with an increase in species and morphological diversification. However, it is possible that certain ecological settings might prevent lineages from diversifying. Arboreality evolved multiple times in vipers, making them ideal organisms for exploring how potentially new ecological opportunities affect their morphology and speciation regimes. Arboreal snakes are frequently suggested to have a very specialized morphology, and being too large, too small, too heavy, or having short tails might be challenging for them. Using trait-evolution models, we show that arboreal vipers are evolving towards intermediate body sizes, with longer tails and more slender bodies than terrestrial vipers. Arboreality strongly constrains body size and circumference evolution in vipers, while terrestrial lineages are evolving towards a broader range of morphological variants. Trait-dependent diversification models, however, suggest similar speciation rates between microhabitats. Thus, we show that arboreality might constrain morphological evolution but not necessarily affect the rates at which lineages generate new species.

KEYWORDS: speciation, divergent selection, snakes, Ornstein–Uhlenbeck

The arboreal Stejneger's Pitviper (Trimeresurus stejnegeri).

Photo: M. Martins 

Laura Rodrigues Vieira de Alencar, Marcio Martins, Gustavo Burin and Tiago Bosisio Quental. 2017. Arboreality Constrains Morphological Evolution but Not Species Diversification in Vipers. Proceedings of the Royal Society B: Biological Sciences. 284(1869)  DOI: 10.1098/rspb.2017.1775 

alencarlaura.weebly.com/publications.html

facebook.com/LauraAlencar10/posts/1593655680711909

    

[Herpetology • 2017] Species Delimitation with Gene Flow: A Methodological Comparison and Population Genomics Approach to Elucidate Cryptic Species Boundaries in Malaysian Torrent Frogs

DOI: 10.1111/mec.14296 

Abstract

Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.

Keywords: Amolops, migration rate, fastsimcoal2, site frequency spectrum, gene flow, single-nucleotide polymorphism 

Kin Onn Chan, Alana M. Alexander, Lee L. Grismer, Yong-Chao Su, Jesse L. Grismer, Evan S. H. Quah and Rafe M. Brown. 2017. Species Delimitation with Gene Flow: A Methodological Comparison and Population Genomics Approach to Elucidate Cryptic Species Boundaries in Malaysian Torrent Frogs.  Molecular Ecology. DOI: 10.1111/mec.14296 

ResearchGate.net/publication/319088398_Species_delimitation_with_gene_flow_a_methodological_comparison_and_population_genomics_approach_to_elucidate_cryptic_species_boundaries_in_Malaysian_Torrent_Frogs

[PaleoOrnithology • 2017] Leucocarbo septentrionalis • Speciation, Range Contraction and Extinction in the Endemic New Zealand King Shag Complex

Leucocarbo septentrionalis

Rawlence, Till, Easton, Spencer, Schuckard, Melville, Scofield, Tennyson, Rayner & Waters, 2017

Kohatu Shag || DOI: 10.1016/j.ympev.2017.07.011 

Highlights

• New Zealand King Shag occupied a ‘relict’ distribution for at least the past 240 years.

• Ancient DNA indicates drop in genetic variability and range shortly after human arrival.

• Leucocarbo from northern New Zealand represent new extinct species, Kohatu Shag.

• New Zealand biodiversity hotspot for Phalacrocoracidae.

Abstract

New Zealand’s endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240 years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications. Our analyses show that the King Shag was formerly widespread around southern coasts of the North Island and the northern parts of the South Island but experienced population and lineage extinctions, and range contraction, probably after Polynesian arrival. This history parallels range contractions of other New Zealand seabirds. Conservation management of the King Shag should take into account this species narrow distribution and probable reduced genetic diversity. Moreover, combined genetic, morphometric and osteological analyses of prehistoric material from mainland New Zealand suggest that the now extinct northern New Zealand Leucocarbo populations comprised a unique lineage. Although these distinctive populations were previously assigned to the King Shag (based on morphological similarities and geographic proximity to modern Leucocarbo populations), we herein describe them as a new species, the Kohatu Shag (Leucocarbo septentrionalis). The extinction of this species further highlights the dramatic impacts Polynesians and introduced predators had on New Zealand’s coastal and marine biodiversity. The prehistoric presence of at least four species of Leucocarbo shag on mainland NZ further highlights its status as a biodiversity hotspot for Phalacrocoracidae.

Keywords: Ancient DNA; Extinct; Holocene fossil; King Shag; Kohatu Shag; Leucocarbo carunculatus; Leucocarbo septentrionalis; New species; New Zealand

Fig. 8. Cranial skeletal elements of the holotype of Kohatu Shag (Leucocarbo septentrionalis; NMNZ S.34434). (a) Lateral view; (b) Dorsal view; (c) Ventral view. 

 Systematic palaeontology

PELECANIFORMES Sharpe, 1891

PHALACROCORACIDAE Reichenbach, 1849

LEUCOCARBO Bonaparte, 1857

 [type species (by subsequent designation, Ogilvie-Grant, 1898) Carbo bougainvillii Lesson, 1837]

LEUCOCARBO SEPTENTRIONALIS  SP. NOV.

English name: Kohatu Shag; Maori name: Kawau Kohatu

Type locality: Tokerau Beach, Doubtless Bay, Northland, New Zealand.

Etymology: septentrionalis from the medieval Latin for northern. This specific name recognises that this was the northernmost New Zealand member of the genus Leucocarbo. The name Kawau Kohatu in Maori is derived from the phrase ‘Te Ao Kohatu’ and means ‘shag [Kawau] from the stone age before our time [Te Ao Kohatu]’. The name recognises the species was found in Holocene fossil deposits of the iwi Ngati Kuri’s tribal area.

Distribution: Formerly of Northland, New Zealand.

Nicolas J. Rawlence, Charlotte E. Till, Luke J. Easton, Hamish G. Spencer, Rob Schuckard, David S. Melville, R. Paul Scofield, Alan J.D. Tennyson, Matt J. Rayner and Jonathan M. Waters. 2017. Speciation, Range Contraction and Extinction in the Endemic New Zealand King Shag Complex.  Molecular Phylogenetics and Evolution. in press. DOI: 10.1016/j.ympev.2017.07.011

Another extinct bird: Northland’s unique shag  blog.tepapa.govt.nz/2017/08/14/another-extinct-bird-northlands-unique-shag via @te_papa

Hiding in plain sight: how we found New Zealand’s newest seabird, the Kōhatu Shag"  sciblogs.co.nz/guestwork/2017/08/14/kohatu-shag   @sciblogsnz 

  

[Mammalogy • 2017] Glaucomys oregonensis • Genetic Data Reveal A Cryptic Species of New World Flying Squirrel

Glaucomys oregonensis  (Bachman, 1839)

DOI: 10.1093/jmammal/gyx055  

Photograph by N. Kerhoulas. NationalGeographic.com

Abstract

The genus Glaucomys (New World flying squirrels) is currently considered to be comprised of 2 species, the northern flying squirrel (G. sabrinus) and the southern flying squirrel (G. volans). We synthesize new information from mitochondrial DNA (mtDNA) control region sequences and microsatellite data to demonstrate that the genus consists of 3, rather than 2 species, and that Glaucomys sabrinus, as currently recognized, is actually composed of 2 separate, apparently non-hybridizing species. Control region mtDNA data from 185 individuals across North America revealed 2 distinct clades embedded within G. sabrinus: a widespread “Continental” lineage and a more geographically restricted “Pacific Coastal” lineage. The geographic distributions of these 2 lineages are largely mutually exclusive, with sympatry observed at only 3 sites in the Pacific Northwest. Analysis of 8 microsatellite loci showed no evidence of hybridization between the 2 lineages of G. sabrinus in the region of sympatry. This lack of gene flow is noteworthy given that populations of the Continental lineage of G. sabrinus have been shown to hybridize with G. volans in southeastern Canada. Finally, phylogenetic analyses and estimates of divergence times show that G. volans and Continental G. sabrinus are actually sister taxa that diverged from one another more recently than either did from Pacific Coastal G. sabrinus. We propose that these observations provide strong evidence for a third, previously unrecognized species of North American flying squirrel, whose geographic range extends along the Pacific Coast from southern British Columbia to southern California. Glaucomys oregonensis (Bachman, 1839), whose type locality is in Oregon, is the senior available name for this taxon. We propose that this newly recognized species be given the common name “Humboldt’s flying squirrel.”

Keywords: cryptic speciation, Glaucomys oregonensis, Glaucomys sabrinus, Glaucomys volans, Humboldt’s flying squirrel, microsatellites, phylogeography, Rodentia, Sciuridae

Brian S. Arbogast, Katelyn I. Schumacher, Nicholas J. Kerhoulas, Allison L. Bidlack, Joseph A. Cook and G. J. Kenagy. 2017. Genetic Data Reveal A Cryptic Species of New World Flying Squirrel: Glaucomys oregonensis.  Journal of Mammalogy. DOI: 10.1093/jmammal/gyx055 

Meet This Newly Discovered Flying Squirrel on.natgeo.com/2qxAX9s via @NatGeo

news.NationalGeographic.com/2017/05/flying-squirrel-new-species-north-america/