Cryptic diversity and non-adaptive radiation of montane New Guinea skinks (Papuascincus; Scincidae)

To and fro in the archipelago: Repeated inter-island dispersal and New Guinea's orogeny affect diversification of Delias, the world's largest butterfly genus

The world's largest butterfly genus Delias, commonly known as Jezebels, comprises ca. 251 species found throughout Asia, Australia, and Melanesia. Most species are endemic to islands in the Indo-Australian Archipelago or to New Guinea and nearby islands in Melanesia, and many species are restricted to montane habitats over 1200 m. We inferred an extensively sampled and well-supported molecular phylogeny of the group to better understand the spatial and temporal dimensions of its diversification. The remarkable diversity of Delias evolved in just ca. 15-16 Myr (crown age). The most recent common ancestor of a clade with most of the species dispersed out of New Guinea ca. 14 Mya, but at least six subsequently diverging lineages dispersed back to the island. Diversification was associated with frequent dispersal of lineages among the islands of the Indo-Australian Archipelago, and the divergence of sister taxa on a single landmass was rare and occurred only on the largest islands, most notably on New Guinea. We conclude that frequent inter-island dispersal during the Neogene-likely facilitated by frequent sea level change-sparked much diversification during that period. Many extant New Guinea lineages started diversifying 5 Mya, suggesting that orogeny facilitated their diversification. Our results largely agree with the most recently proposed species group classification system, and we use our large taxon sample to extend this system to all described species. Finally, we summarize recent insights to speculate how wing pattern evolution, mimicry, and sexual selection might also contribute to these butterflies' rapid speciation and diversification.

New Insights into the Variation and Admixture of the Cave-Dwelling Spider Trogloneta yunnanensis in South China Karst

Subterranean karst caves can contain unexpected biodiversity, but few studies related to spider population genetics have been conducted in the karst area of Southern China. In this study, we investigated the population genetic structure of Trogloneta yunnanensis (Song & Zhu, 1994) based on 73 spider samples from six underground populations in South China Karst. Population genetic structure analysis showed a clear divergence (FST > 0.9 and Nm < 0.05) among populations according to mitochondrial genes. The phylogenetic gene tree constructed by BI and ML methods recovered six geographic clades. Divergence time estimation indicated that the divergence of these six populations can be traced back to the late Pleistocene. We supposed that the geographic isolation led to the extreme population structure. According to this study and previous studies about troglobites living in this region, the subterranean habitats of the Yunnan-Guizhou Plateau may contain many organisms with similar genetic structures. The subterranean biodiversity in the karst area of Southern China needs to be re-evaluated and protected.

Fruit Size in Indo-Malayan Island Plants Is More Strongly Influenced by Filtering than by In Situ Evolution

AbstractCommunity trait assembly, the formation of distributions of phenotypic characteristics across coexisting species, can occur via two main processes: filtering of trait distributions from the regional pool and in situ phenotypic evolution in local communities. But the relative importance of these processes remains unclear, largely because of the difficulty in determining the timing of evolutionary trait changes and biogeographic dispersal events in phylogenies. We assessed evolutionary and biogeographic transitions in woody plant species across the Indo-Malay archipelago, a series of island groups where the same plant lineages interact with different seed disperser and seed predator assemblages. Fruit size in 2,650 taxa spanning the angiosperm tree of life tended to be smaller in the Sulawesi and Maluku island groups, where frugivores are less diverse and smaller bodied, than in the regional source pool. While numerous plant lineages (not just small-fruited ones) reached the isolated islands, colonists tended to be the smaller-fruited members of each clade. Nearly all of the evolutionary transitions to smaller fruit size predated, often substantially, organismal dispersal to the islands. Our results suggest that filtering rather than within-island evolution largely determined the distribution of fruit sizes in these regions.

New Guinea uplift opens ecological opportunity across a continent

Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.

A new species of New Guinea Worm-Eating Snake (Serpentes, Elapidae, Toxicocalamus Boulenger, 1896) from Western Highlands Province, Papua New Guinea

We describe a new species of New Guinea Worm-Eating Snake (Elapidae: Toxicocalamus) from a specimen in the reptile collection of the Papua New Guinea National Museum and Art Gallery. Toxicocalamus longhagensp. nov. can be easily distinguished from other species of this genus by the presence of paired subcaudals, a preocular scale unfused from the prefrontal scale, a prefrontal distinct from the internasal scale that contacts the supralabials, a single large posterior temporal and two postocular scales. The new taxon is currently known only from one specimen, which was collected from Mt. Hagen Town in Western Highlands Province, Papua New Guinea in 1967. The new species was originally identified as T. loriae, but the unique head scalation and postfrontal bone morphology revealed through micro-computed tomography scanning easily distinguish the new species from T. loriaesensu stricto. This is the first species of this genus described from Western Highlands Province.

Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation

Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome‐wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai‐Tibetan plateau between lowland south‐eastern Chinese R. d. fohkienensis and high‐altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well‐known avian migratory divide, where western lineages take a western migration route around the Qinghai‐Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.

Revision of the montane New Guinean skink genus Lobulia (Squamata: Scincidae), with the description of four new genera and nine new species

The skink genus Lobulia is endemic to New Guinea, the largest and highest tropical island in the world. Lobulia and its related genera represent an important component of the montane herpetofauna of New Guinea, but it remains understudied and poorly known. We here provide the first, large-scale, systematic revision of Lobulia, using molecular phylogenetic and morphological comparisons to assess the monophyly of the genus and the diversity of species within it. We find that Lobulia, as currently defined, is polyphyletic. The eight species currently assigned to it form three clades. Furthermore, many specimens from New Guinea of unknown specific affinity are genetically and morphologically distinct from each other. Based on these data, we re-diagnose Lobulia and two of its closely related genera, Prasinohaema and Papuascincus. We erect four new genera (Alpinoscincus gen. nov., Nubeoscincus gen. nov., Ornithuroscincus gen. nov. and Palaia gen. nov.) to address the problem of polyphyly and describe nine new species Lobulia fortis sp. nov., Lobulia huonensis sp. nov., Loublia marmorata sp. nov., Lobulia vogelkopensis sp. nov., Ornithuroscincus bengaun sp. nov., Ornithuroscincus inornatus sp. nov., Ornithuroscincus pterophilus sp. nov., Ornithuroscincus shearmani sp. nov. and Ornithuroscincus viridis sp. nov. We supplement this taxonomic revision by investigating the biogeographic history of Lobulia s.l. and find evidence for a large radiation in the accreted terranes of New Guinea, with multiple independent colonizations of montane habitats and subsequent recolonization of lowland habitats. Our study reinforces the uniqueness and richness of the montane herpetofauna of New Guinea and the importance of mountains to biodiversity in the Tropics.

New Guinean orogenic dynamics and biota evolution revealed using a custom geospatial analysis pipeline

BACKGROUND

The New Guinean archipelago has been shaped by millions of years of plate tectonic activity combined with long-term fluctuations in climate and sea level. These processes combined with New Guinea's location at the tectonic junction between the Australian and Pacific plates are inherently linked to the evolution of its rich endemic biota. With the advent of molecular phylogenetics and an increasing amount of geological data, the field of New Guinean biogeography begins to be reinvigorated.

RESULTS

We inferred a comprehensive dated molecular phylogeny of endemic diving beetles to test historical hypotheses pertaining to the evolution of the New Guinean biota. We used geospatial analysis techniques to compare our phylogenetic results with a newly developed geological terrane map of New Guinea as well as the altitudinal and geographic range of species ( https://arcg.is/189zmz ). Our divergence time estimations indicate a crown age (early diversification) for New Guinea Exocelina beetles in the mid-Miocene ca. 17 Ma, when the New Guinean orogeny was at an early stage. Geographic and geological ancestral state reconstructions suggest an origin of Exocelina ancestors on the eastern part of the New Guinean central range on basement rocks (with a shared affinity with the Australian Plate). Our results do not support the hypothesis of ancestors migrating to the northern margin of the Australian Plate from Pacific terranes that incrementally accreted to New Guinea over time. However, our analyses support to some extent a scenario in which Exocelina ancestors would have been able to colonize back and forth between the amalgamated Australian and Pacific terranes from the Miocene onwards. Our reconstructions also do not support an origin on ultramafic or ophiolite rocks that have been colonized much later in the evolution of the radiation. Macroevolutionary analyses do not support the hypothesis of heterogeneous diversification rates throughout the evolution of this radiation, suggesting instead a continuous slowdown in speciation.

CONCLUSIONS

Overall, our geospatial analysis approach to investigate the links between the location and evolution of New Guinea's biota with the underlying geology sheds a new light on the patterns and processes of lineage diversification in this exceedingly diverse region of the planet.

Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics

Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80 K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of π_a/π_s and K_a/K_s with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.

Elevation is a stronger predictor of morphological trait divergence than competition in a radiation of tropical lizards

Adaptations for efficient performance are expected to shape animal morphology based on selection for microhabitat use and ecological forces. The presence of competitor species is predicted to cause niches to contract and enhance trait divergence. Therefore, increased species richness is expected to lead to greater trait divergence, and to result in reduced overlap and similarity between morphologies of sympatric species. We examined patterns of morphospace occupancy and partitioning in the skink fauna of New Guinea, the world's largest tropical island. Because skink species richness is largely decoupled from elevation in New Guinea, we could examine the effects of both factors (as proxies for competition and abiotic conditions), on morphospace occupancy and partitioning. We measured 1,860 specimens from 79 species of skinks throughout Papua New Guinea, and examined their morphospace occupancy in a spatial context. We calculated, for each assemblage within equal-area cells, the volume of morphospace occupied by all skinks, the mean volume occupied per species, and the mean distance and overlap between all species pairs. We then examined whether these metrics are related to species richness and elevation. Elevation is a stronger predictor of morphospace occupancy than species richness. As elevation increases, intraspecific variation decreases and morphologies become more similar to each other such that overall morphospace occupancy decreases. Highland skinks are, on average, smaller, thinner and shorter limbed than lowland species. We hypothesise that harsh climates in the New Guinea highland habitats impose strong selection on skinks to occupy specific areas of morphospace that facilitate efficient thermoregulation in suboptimal thermal conditions. We conclude that the effect of competition on trait divergence on a community and assemblage scale is eclipsed by abiotic selection pressures in these harsh environments.