Phylogeny of dwarf geckos of the genus Lygodactylus (Gekkonidae) in the Western Indian Ocean.

Diurnal dwarf geckos of the genus Lygodactylus are distributed in tropical and subtropical regions and live in highly diverse habitats. The genus currently comprises 79 species and several candidates for new species or subspecies. Most of these taxa occur in Sub-Saharan Africa and Madagascar, with only two described species in South America. Although the main center of diversity of Lygodactylus currently is Africa, the genus probably has a Malagasy origin, followed by two or three independent transoceanic dispersal events between Madagascar and Africa and one trans-Atlantic dispersal from Africa to South America. A few species colonised islands in the Western Indian Ocean belonging to the Zanzibar Archipelago and to the Îles Éparses. Here we examined L. grotei pakenhami from Pemba Island, L. insularis from Juan de Nova, and L. verticillatus from Europa Island to clarify their taxonomic status and their origin. Concerning L. grotei pakenhami and L. insularis, preceding studies pointed to a relation to species of the African L. capensis group. In contrast, L. verticillatus on Europa Island is considered to be conspecific with Malagasy populations. Therefore, we conducted a phylogenetic study of the African L. capensis group and the Malagasy L. verticillatus group, and examined color pattern, selected morphological characters and two mitochondrial markers (ND2 for African and 16S rRNA for Malagasy Lygodactylus). Lygodactylus grotei pakenhami from Pemba and L. grotei from mainland Africa cannot be distinguished by their scalation, but their reciprocal monophyly suggested by mitochondrial DNA, conspicuously different coloration (both in adults and hatchlings) and their high genetic distances (16.3% in ND2) support the hypothesis that these taxa represent two distinct species. Consequently, we elevate L. grotei pakenhami to species level, as Lygodactylus pakenhami Loveridge, 1941. Lygodactylus pakenhami is endemic to Pemba Island which was possibly separated from the African mainland during the late Miocene or Early Pliocene (6 million years ago). The simplest explanation for the existence of L. pakenhami on Pemba is vicariance. A recent, human-mediated transportation is excluded, as the molecular data clearly indicate a longer period of isolation. Lygodactylus insularis has been supposed to be related to the taxa 'capensis' or 'grotei'. However, it is impossible to discern the relationship of L. insularis, L. capensis and L. grotei by means of scalation or coloration alone. Our molecular phylogenetic analyses reveal that L. insularis is embedded within the L. capensis group, clearly indicating its African origin. The single gene (ND2) as well as the multigene analyses fully support a closer common origin of L. insularis and L. capensis than of L. insularis and L. grotei. However, the position of L. insularis within the clade formed by L. insularis, L. nyaneka, L. capensis sensu stricto and six L. aff. capensis groups is not clearly resolved. Lygodactylus insularis is endemic on Juan de Nova Island, an old low elevation atoll. That all L. insularis mitochondrial sequences are very similar to each other and together form a monophyletic lineage is in agreement with the hypothesis of a single dispersal event to the island. For the L. verticillatus population from Europa Island our mitochondrial data suggest close relationships to conspecific samples from the coastal regions of south-western Madagascar. As we found no relevant morphological or genetic differences between the insular and the Malagasy populations of L. verticillatus, and no remarkable genetic variation within the monophyletic lineage on Europa, we suggest a single, very recent dispersal event, perhaps human-mediated. Although the genus Lygodactylus colonised Africa, islands in the Gulf of Guinea, South America and some islands in the Western Indian Ocean, it seems-compared to other lizard genera-to be only moderately successful in transoceanic long-distance dispersal.

Melanesia holds the world's most diverse and intact insular amphibian fauna.

Identifying hotspots of biological diversity is a key step in conservation prioritisation. Melanesia-centred on the vast island of New Guinea-is increasingly recognised for its exceptionally species-rich and endemic biota. Here we show that Melanesia has the world's most diverse insular amphibian fauna, with over 7% of recognised global frog species in less than 0.7% of the world's land area, and over 97% of species endemic. We further estimate that nearly 200 additional candidate species have been discovered but remain unnamed, pointing to a total fauna in excess of 700 species. Nearly 60% of the Melanesian frog fauna is in a lineage of direct-developing microhylids characterised by smaller distributions than co-occurring frog families, suggesting lineage-specific high beta diversity is a key driver of Melanesian anuran megadiversity. A comprehensive conservation status assessment further highlights geographic concentrations of recently described range-restricted threatened taxa that warrant urgent conservation actions. Nonetheless, by world standards, the Melanesian frog fauna is relatively intact, with 6% of assessed species listed as threatened and no documented extinctions; and thus it provides an unparalleled opportunity to understand and conserve a megadiverse and relatively intact insular biota.

FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales.

Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait  kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.

A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation.

The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35-22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches.

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements.

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread "generalist" clades. This is especially true in Australasia, where monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately "derived" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements (UCEs) to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyze multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme addresses four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic, and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesi's L. iskandari as the sister taxon to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high-elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister taxon relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not grouped with Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our resolved and strongly supported phylogeny, we present a new classification emphasizing the most inclusive, original generic name (Gekko) for these ~60 taxa, arranged into seven subgenera.

A new miniature Melanesian Forest Frog (Ceratobatrachidae: Cornufer) from New Britain Island, constituting the first record of the subgenus Batrachylodes from outside of the Solomon Archipelago.

We describe a new species of Cornufer, subgenus Batrachylodes, from high-elevation forests of New Britain Island in the Bismarck Archipelago of Eastern Melanesia. The new species, Cornufer exedrus sp. nov., is a biogeographically disjunct member of the Batrachylodes clade, representing the first record of the subgenus from outside of the Solomon Archipelago. The new species is a small terrestrial form from dense, closed-canopy forests above 1500 meters elevation in the Nakanai Mountains of eastern New Britain. It differs from its closest relatives, the other members of the subgenus Batrachylodes, on the basis of its minute body size, degree of digital disc expansion, reduced subdigital tuberculation, color pattern, and other traits related to its small size. We also provide a description of the new species' simple advertisement call. The diversity of ceratobatrachid frogs of the Bismarck Archipelago is most likely still underestimated despite several recent surveys. Our understanding of evolutionary trends and species boundaries in the subgenus Batrachylodes currently is hampered by lack of genetic samples and call recordings corresponding to voucher specimens of the endemic species of Bougainville Island.

Lizards of the lost arcs: mid-Cenozoic diversification, persistence and ecological marginalization in the West Pacific.

Regions with complex geological histories often have diverse and highly endemic biotas, yet inferring the ecological and historical processes shaping this relationship remains challenging. Here, in the context of the taxon cycle model of insular community assembly, we investigate patterns of lineage diversity and habitat usage in a newly characterized vertebrate radiation centred upon the world's most geologically complex insular region: island arcs spanning from the Philippines to Fiji. On island arcs taxa are ecologically widespread, and provide evidence to support one key prediction of the taxon cycle, specifically that interior habitats (lowland rainforests, montane habitats) are home to a greater number of older or relictual lineages than are peripheral habitats (coastal and open forests). On continental fringes, however, the clade shows a disjunct distribution away from lowland rainforest, occurring in coastal, open or montane habitats. These results are consistent with a role for biotic interactions in shaping disjunct distributions (a central tenant of the taxon cycle), but we find this pattern most strongly on continental fringes not islands. Our results also suggest that peripheral habitats on islands, and especially island arcs, may be important for persistence and diversification, not just dispersal and colonization. Finally, new phylogenetic evidence for subaerial island archipelagos (with an associated biota) east of present-day Wallace's Line since the Oligocene has important implications for understanding long-term biotic interchange and assembly across Asia and Australia.

Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs.

The microhylid frog genus Kaloula is an adaptive radiation spanning the edge of the Asian mainland and multiple adjacent island archipelagos, with much of the clade's diversity associated with an endemic Philippine radiation. Relationships among clades from the Philippines, however, remain unresolved. With ultraconserved element (UCE) and mitogenomic data, we identified highly supported differences in topology and areas of poor resolution, for each marker set. Using the UCE data, we then identified possible instances of contemporary hybridization, past introgression, and incomplete lineage sorting (ILS) within the Philippine Kaloula. Using a simulation approach, and an estimate of the Philippine Kaloula clade origin (12.7-21.0 mya), we demonstrate that an evolutionary history including inferred instances of hybridization, introgression, and ILS leads to phylogenetic reconstructions that show concordance with results from the observed mitogenome and UCE data. In the process of validating a complex evolutionary scenario in the Philippine Kaloula, we provide the first demonstration of the efficacy of UCE data for phylogenomic studies of anuran amphibians.

Tectonic collision and uplift of Wallacea triggered the global songbird radiation.

Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.

The Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards.

BACKGROUND: The Indian Tectonic Plate split from Gondwanaland approximately 120 MYA and set the Indian subcontinent on a ~ 100 million year collision course with Eurasia. Many phylogenetic studies have demonstrated the Indian subcontinent brought with it an array of endemic faunas that evolved in situ during its journey, suggesting this isolated subcontinent served as a source of biodiversity subsequent to its collision with Eurasia. However, recent molecular studies suggest that Eurasia may have served as the faunal source for some of India's biodiversity, colonizing the subcontinent through land bridges between India and Eurasia during the early to middle Eocene (~35-40 MYA). In this study we investigate whether the Draconinae subfamily of the lizard family Agamidae is of Eurasian or Indian origin, using a multi locus Sanger dataset and a novel dataset of 4536 ultraconserved nuclear element loci. RESULTS: Results from our phylogenetic and biogeographic analyses revealed support for two independent colonizations of India from Eurasian ancestors during the early to late Eocene prior to the subcontinent's hard collision with Eurasia. CONCLUSION: These results are consistent with other faunal groups and new geologic models that suggest ephemeral Eocene land bridges may have allowed for dispersal and exchange of floras and faunas between India and Eurasia during the Eocene.

Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species.

We describe two new species of morphologically cryptic monitor lizards (genus Varanus) from the Philippine Archipelago:  Varanus dalubhasa sp. nov. and V. bangonorum sp. nov. These two distinct evolutionary lineages are members of the V. salvator species complex, and historically have been considered conspecific with the widespread, northern Philippine V. marmoratus. However, the new species each share closer phylogenetic affinities with V. nuchalis (and potentially V. palawanensis), than either does to one another or to V. marmoratus. Divergent from other recognized species within the V. salvator Complex of water monitors by as much as 3.5% pairwise genetic distance, these lineages are also distinguished by unique gular coloration, metrics of body size and scalation, their non-monophyly with "true" V. marmoratus, and insular allopatric distributions, suggesting biogeographically distinct and unique evolutionary histories. We compare the new species with the most geographically proximate and phenotypically relevant lineages.  Although we show that these new taxa are nearly indistinguishable morphologically from V. marmoratus, both species can be readily distinguished from their closest relatives (each's respective sister taxon, V. palawanensis and V. nuchalis) by traditional morphological characters.  Our findings underscore the high herpetological diversity and biogeographical complexity of vertebrates in the Philippines, and further emphasize the need for detailed study of species-level diversity, mechanisms of reproductive isolation, gene flow, and biologically relevant boundaries between taxa within the V. salvator Complex.

A molecular phylogeny of Afromontane dwarf geckos (Lygodactylus) reveals a single radiation and increased species diversity in a South African montane center of endemism.

Afromontane habitats throughout eastern sub-Saharan Africa support remarkable levels of microendemism. However, despite being the subject of decades of research interest, biogeographical patterns of diversification throughout this disjunct montane system still remain largely unknown. We examined the evolutionary relationships of diurnal dwarf geckos (Lygodactylus) from several Afromontane regions throughout southeastern Africa, focusing primarily on two species groups (rex and bonsi groups). Using both mitochondrial and nuclear markers, we generate a molecular phylogeny containing all members of the rex and bonsi groups, to evaluate the monophyly of these groups along with previous biogeographic hypotheses suggesting independent southward invasions into the greater Drakensberg Afromontane center of endemism in northeastern South Africa by each group. Our results provide no support for these taxonomic and biogeographic hypotheses, and instead reveal geographically circumscribed patterns of diversification. One clade is restricted to the highlands of southern Malawi and northern Mozambique and the other to the greater Drakensberg region of northeastern South Africa and Swaziland. Interestingly, L. bernardi from the Nyanga Highlands of eastern Zimbabwe is nested within the primarily savanna-dwelling capensis group. We use Bayesian species delimitation methods to evaluate species limits within the greater Drakensberg clade, which support the elevation of the subspecies of L. ocellatus and L. nigropunctatus, thus bringing the total to eight species within a relatively confined geographic area. These results further highlight the greater Drakensberg Afromontane region as both an important center of endemism, as well as a center of diversification contributing to the accumulation of southern Africa's rich species diversity.

A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated 'sky island' of northern Mozambique.

A new species of high elevation dwarf gecko (Gekkonidae: Lygodactylus) is described from Mount Namuli, northern Mozambique. This new species is distinguished from other closely related species in the genus Lygodactylus by body size, scalation, and color, and is genetically divergent from congeners. The species is most similar genetically and morphologically to Lygodactylus rex, the King Dwarf Gecko, which is endemic to Mount Mulanje, Malawi. Mount Mulanje and Mount Namuli are two of several understudied inselbergs forming the southern limit of the Afromontane archipelago in Malawi and Mozambique. The sister taxon relationship of the dwarf gecko species on Mount Mulanje and Mount Namuli illustrates the historical biogeographic connections between these inselbergs, a pattern which is emerging with continued work in this region. The discovery of this new species adds to a growing list of species unique to Mount Namuli, and further establishes this montane region as a conservation priority.