Drivers of an epic radiation: the role of climate and islands in species diversification and reproductive-mode evolution of Old-World tree frogs

Although large diversifications of species occur unevenly across space and evolutionary lineages, the relative importance of their driving mechanisms, such as climate, ecological opportunity and key innovations, remains poorly understood. Here, we explore the remarkable diversification of rhacophorid frogs, which represent six percent of global amphibian diversity, utilize four distinct reproductive modes, and span a climatically variable area across mainland Asia, associated continental islands, and Africa. Using a complete species-level phylogeny, we find near-constant diversification rates but a highly uneven distribution of species richness. Montane regions on islands and some mainland regions have higher phylogenetic diversity and unique assemblages of taxa; we identify these as cool-wet refugia. Starting from a centre of origin, rhacophorids reached these distant refugia by adapting to new climatic conditions (niche evolution-dominant), especially following the origin of key innovations such as terrestrial reproduction (in the Late Eocene) or by dispersal during periods of favourable climate (niche conservatism-dominant).

Genome of a middle Holocene hunter-gatherer from Wallacea

Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939–7751 calibrated years before present (yr cal bp; present taken as ad 1950), and Gua Cha in Malaysia (4.4–4.2 kyr cal bp)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia–New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3–7.2 kyr cal bp at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the ‘Toalean’ technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

The robustness of a simple dynamic model of island biodiversity to geological and eustatic change

Aim: Biodiversity on islands is affected by various geo-physical processes and sea-level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, followed by a decline as islands shrink. Continental islands have species upon formation (when disconnected from the mainland) and may have transient land-bridge connections. Theoretical predictions for the effects of these geo-processes on rates of colonisation, speciation and extinction have been proposed, but methods of phylogenetic inference assume only oceanic island scenarios without accounting for island ontogeny, sea-level changes or past landmass connections. Here, we analyse to what extent ignoring geodynamics affects the inference performance of a phylogenetic island model, DAISIE, when confronted with simulated data that violate its assumptions. Location: Simulation of oceanic and continental islands. Methods: We extend the DAISIE simulation model to include: area-dependent rates of colonisation and diversification associated with island ontogeny and sea-level fluctuations, and continental islands with biota present upon separation from the mainland, and shifts in rates to mimic temporary land-bridges. We quantify the error made when geo-processes are not accounted for by applying DAISIE's inference method to geodynamic simulations. Results: We find that the robustness of the model to dynamic island area is high (error is small) for oceanic islands and for continental islands that have been separated for a long time, suggesting that, for these island types, it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of DAISIE is low, and inference results should not be trusted. Main conclusions: This study highlights that under a large proportion of island biogeographic geo-scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring development of a new inference model.

Genetic diversity and structure of Saussurea polylepis (Asteraceae) on continental islands of Korea: Implications for conservation strategies and management

Saussurea polylepis Nakai is an herbaceous perennial endemic to Korea and is highly restricted to several continental islands in the southwestern part of the Korean Peninsula. Given its very narrow geographical distribution, it is more vulnerable to anthropogenic activities and global climate changes than more widely distributed species. Despite the need for comprehensive genetic information for conservation and management, no such population genetic studies of S. polylepis have been conducted. In this study, genetic diversity and population structure were evaluated for 97 individuals from 5 populations (Gwanmaedo, Gageodo, Hongdo, Heusando, and Uido) using 19 polymorphic microsatellites. The populations were separated by a distance of 20–90 km. We found moderate levels of genetic diversity in S. polylepis (Ho = 0.42, He = 0.43). This may be due to long lifespans, outcrossing, and gene flow, despite its narrow range. High levels of gene flow (Nm = 1.76, mean Fst = 0.09), especially from wind-dispersed seeds, would contribute to low levels of genetic differentiation among populations. However, the small population size and reduced number of individuals in the reproductive phase of S. polylepis can be a major threat leading to inbreeding depression and genetic diversity loss. Bayesian cluster analysis revealed three significant structures at K = 3, consistent with DAPC and UPGMA. It is thought that sea level rise after the last glacial maximum may have acted as a geographical barrier, limiting the gene flow that would lead to distinct population structures. We proposed the Heuksando population, which is the largest island inhabited by S. polylepis, as a source population because of its large population size and high genetic diversity. Four management units (Gwanmaedo, Gageodo, Hongdo-Heuksando, and Uido) were suggested for conservation considering population size, genetic diversity, population structure, unique alleles, and geographical location (e.g., proximity).

Behavioral context shapes vocal sequences in two anuran species with different repertoire sizes

Acoustic signals in animals serve to convey context-dependent information to receivers. Birds and mammals combine diverse sounds into complex sequences to communicate, but these sequences largely remain understudied in other taxa. Anuran vocalizations are a prominent feature of their life history, and function in defense of territories and to attract mates. However, despite the spectacular diversity of anurans in tropical regions of the world, vocal diversity and communication strategies remain relatively poorly studied. Specifically, studies of vocal sequences and context-dependent vocal patterns in frogs remain few. Here, we investigated the context-dependent vocal repertoire and the use of vocal sequences by two anuran species belonging to different lineages, both endemic to the hyper-diverse Western Ghats of India. By recording vocal sequences both when frogs were alone and in the presence of a territorial rival, we present evidence that both species modify their vocal repertoire according to context. Specifically, one species appends notes to generate more complex sequences, whereas the other shifts to different note types, resulting in different sequences for different contexts. Thus, despite differences in repertoire size, both frog species are capable of adjusting the temporal sequence of vocalizations to communicate in different contexts. This study highlights the need for further studies of insular frogs, to understand how diversification across these continental islands has influenced the evolution of vocal repertoires, vocal sequence patterns and communication systems.Lay SummaryAnimals employ complex sequences of acoustic signals to communicate in diverse behavioral contexts. Here, we demonstrate that two frog species with different vocal repertoires both modify the sequence of note emissions in the presence of a territorial rival. These patterns demonstrate that anurans are capable of complex shifts in the patterns of their vocalization, to communicate different messages to different receivers. Our findings demonstrate the value of studying behavioral diversity in tropical regions.

Pristinity, degradation and replacement: The three dimensions of human impact on island vegetation

This paper presents three extreme examples of the potential consequences of human settlement on the vegetation of oceanic and continental islands. The Neotropical Pantepui continental archipelago of sky islands is an example of pristinity, due to the almost nonexistent human impact that results from the remoteness and inaccessibility of these islands as well as the lack of natural resources to exploit. Easter Island is used to illustrate total vegetation degradation by deforestation and the exhaustion of natural resources, which has transformed the island into badlands with no signs of recovery. The Azores Islands have been chosen to illustrate replacement as, after initial postsettlement deforestation and extractive practices, a further transformative phase consisting of creating an almost totally anthropogenic vegetation with mostly exotic species occurred. The paper describes in some detail the developments of each case and the historical context in which they took place using historical, archeological and paleoecological evidence. Many intermediate states are possible among these three extremes, which can be represented with a ternary diagram (the PDR diagram), which is useful for characterizing the state of each island or archipelago in terms of human impact on terrestrial ecosystems and informing conservation and restoration practices.

Annotated list of island lady beetles from Chile (Coleoptera: Coccinellidae)

We provide a list of coccinellids (Coleoptera: Coccinellidae) species from the island territories of Chile. We report a total of 68 records, coming from ten islands, including 42 species corresponding to more than 35% of the species of the country. This paper presents the first Coccinellidae records for the Islas Desventuradas, Isla Mocha and Isla Tenglo. Contrary to what has been reported on other islands and other taxonomic groups in Chilean islands, the level of coccinellid endemism is low (8%), with only one and two species endemic to the Juan Fernández archipelago and Isla de Chiloé, respectively, and probably a fourth species from the Isla Grande de Tierra del Fuego. The presence of species with worldwide distribution and of agricultural relevance is strong in the Chilean oceanic islands, particularly in Rapa Nui. The fauna of the continental islands is very similar to the one in the nearby continental areas and composed of native species. Further surveys of Coccinellidae and other insects are required for the islands of Chile, especially for several of them in which there are no records.

The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian

Background: Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancient oceanic archipelagos. Here, we focus on the granitic islands of the Seychelles, which are unusual among island systems because they have been isolated for a long time and are home to a monophyletic radiation of caecilian amphibians that has been separated from its extant sister lineage for ca. 65 – 62 Ma. We selected the most widespread Seychelles caecilian species, Hypogeophis rostratus, to investigate intraspecific morphological and genetic (mitochondrial and nuclear) variation across the archipelago (782 samples from nine islands) to identify patterns and test processes that shaped their evolutionary history within the Seychelles.Results: Overall a signal of strong geographic structuring with distinct northern- and southern-island clusters were identified across all datasets. We suggest that these distinct groups have been isolated for ca. 1.26 Ma years without subsequent migration between them. Populations from the somewhat geographically isolated island of Frégate showed contrasting relationships to other islands based on genetic and morphological data, clustering alternatively with northern-island (genetic) and southern-island (morphological) populations.Conclusions: Although variation in H. rostratus across the Seychelles is explained more by isolation-by-distance than by adaptation, the genetic-morphological incongruence for affinities of Frégate H. rostratus might be caused by local adaptation over-riding the signal from their vicariant history. Our findings highlight the need of integrative approaches to investigate fine-scale geographic structuring to uncover underlying diversity and to better understand evolutionary processes on ancient, continental islands.