Onset Of Diversification Research Articles

Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth–death skyline model

The current status of the Sino-Himalayan region as a biodiversity hotspot, particularly for flora, has often been linked to the uplift of the Sino-Tibetan Plateau and Himalayan and Hengduan Mountains. However, the relationship between the topological development of the region and the onset of diversification is yet to be confirmed. Here, we apply Bayesian phylodynamic methods to a large phylogeny of angiosperm species from the Sino-Himalayas to infer changes in their rates of evolution through time. We find strong evidence for high diversification rates in the Paleocene, late Miocene and Pliocene, and for negative diversification rates in the Quaternary driven by an increase in extinction rates. Our analyses suggest that changes in global palaeotemperatures are unlikely to be a driving force for these rate shifts. Instead, the collision of the Indian continent with Eurasia and coeval topographic change in the Sino-Himalayas, the Miocene Grassland Expansion and the impact of Pleistocene glaciations on this altitudinally variable region may have driven these rates. We also demonstrate the strong influence of the choice of change times on the shape of inferred piecewise-constant trajectories in Bayesian phylodynamics, and advocate for the use of prior information when making this decision.

Phylogenomics and a revised tribal classification of subfamily Dipterocarpoideae (Dipterocarpaceae)

AbstractDipterocarpoideae, the largest subfamily in the Meranti family (Dipterocarpaceae) are an ecologically dominant group of trees throughout much of wet tropical Asia. Increasing anthropogenic pressures on this economically important tree family make it essential to resolve their complex evolutionary relationships and understand the distribution of genetic diversity throughout the family and distribution range. Dipterocarpaceae have been the focal group in a wide range of studies, owing to their economic value, importance in historical biogeography and key role in the evolution of the Asian tropical forest biome. Despite this, persistent taxonomic and evolutionary questions remain, ranging from questions on the geographic origin, sequence of dispersal and the identification of diagnostic characters to circumscribe proper evolutionary groups. Here we present a comprehensive phylogenomic hypothesis for Dipterocarpoideae, based on the analyses of plastome and nuclear cistron (NRC) data, and provide an in‐depth review on the validity of morphological characters underlying the new tribal classification proposed here for the subfamily. Phylogenomic relationships were inferred using maximum likelihood and Bayesian approaches. Estimates of origin and onset of diversification in major clades and lineages were reconstructed using plastome, nuclear and combined datasets. Results of the separate and combined genomic datasets partly corroborate elements of previous classification systems (with improved support at all levels for major clades) but provide strong support for revising the tribal classification of the subfamily into four main clades: Dipterocarpeae (Dipterocarpus), Dryobalanopseae (Dryobalanops), Shoreeae (Hopea,Neobalanocarpus,Parashorea, and all parts of a polyphyleticShorea) and Vaterieae (including all other presently accepted Dipterocarpoideae genera). Multi‐fossil‐dated divergence time estimation suggests Vaterieae first originated in the Late Cretaceous, followed by Dipterocarpeae, with subsequent rise of the Dryobalanopseae and Shoreeae in the Eocene. Diversification of all tribes commenced before the Early Miocene. Our results provide strong support for the position ofNeobalanocarpus heimii,Parashoreaand (sub‐)sections of the generaAnisoptera,Hopea,ShoreaandVatica. Hypotheses on the origin ofNeobalanocarpus heimiiby intergeneric hybridisation betweenAnthoshorea(maternally inherited) andHopea(paternally inherited) species were corroborated. Finally, our study provides support for future revisionary changes: (1) the elevation to generic rank of sections inShorea; and (2) revising the infrageneric classification ofHopeaas all (sub‐)sections were recovered as not monophyletic.

Following the Mangroves: diversification in the banded lampeye Aplocheilichthys spilauchen (Duméril, 1861) (Cyprinodontiformes: Procatopodidae) along the Atlantic coast of Africa.

Available ecological information, an extensive distributional range, conflicting osteological data, and a proposed early Miocene origin provide the impetus for the present study which investigates genetic structuring, biogeographic, and phylogenetic relationships within the Aplocheilichthys spilauchen lineage. Through the analysis of the mitochondrial gene COI, species delimitation methods (ABGD, GB, GMYC, bPTP) were applied, recognizing 6–7 OTUs with absolute pairwise genetic distances ranging between 8 and 22%. The onset of diversification is estimated to be within the middle Miocene and both dispersal and vicariance-shaped A. spilauchen diversity and distribution, as suggested by time-calibrated and ancestral range reconstruction (S-DIVA) analyses. We report for the first time, a pattern of diversification within a lineage of brackish water fish that is concordant with the historical distribution of coastal mangroves forests, shaped by a series of historical events that likely affected forest cover since the middle Miocene (e.g. major climate shifts and sea-level fluctuations, onset of the modern Congo River outlet, increased volcanism in the Cameroon Volcanic Line).Supplementary informationThe online version of this article (doi:10.1007/s10750-020-04497-3) contains supplementary material, which is available to authorized users.

Diversification of epizoic freshwater limpets in ancient lakes on Sulawesi, Indonesia: Coincidence or coevolution?

The set of ancient lakes on Sulawesi, Indonesia, represents a unique global hotspot of aquatic biodiversity. These lakes have been recognized widely because of their high number of endemic species with specialized and distinctive morphological characters, life history and ecological adaptations. An interesting case of unusual life history involving brood care exists in the planorbid limpets of the genus Protancylus, which live exclusively as epizoans on the endemic pachychilid gastropod Tylomelania. We aimed to unravel the evolutionary and phylogeographical patterns of Protancylus from the Malili lakes and Lake Poso using two mitochondrial markers in an integrated framework that includes morphological, life-history and ecological data. At least three species of Protancylus evolved allopatrically, with a newly recognized species occurring in lakes Matano and Mahalona. All species are characterized by low morphological variation, shared life-history traits including a unique reproduction strategy. Our genetic data indicates that a drift-based geographic speciation mode correlates with the present distribution pattern. The initial diversification significantly predates the ages of the respective lakes and the lineages of Protancylus are significantly older than their corresponding Tylomelania ‘hosts’. The deep split between P. pileolus of Lake Poso and the populations in the Malili lakes is remarkable and hints to a very early separation in a time frame when Sulawesi reached its current composition. As colonization and onset of diversification is strikingly different in Tylomelania and the epizoic Protancylus, co-evolutionary components in this association can be excluded and both evolved largely independently. We discuss and compare our findings to other invertebrate assemblages in the ancient lakes of Sulawesi.

Geological and Climatic Factors Affect the Population Genetic Connectivity in Mirabilis himalaica (Nyctaginaceae): Insight From Phylogeography and Dispersal Corridors in the Himalaya-Hengduan Biodiversity Hotspot.

The genetic architecture within a species in the Himalaya-Hengduan Mountains (HHM) region was considered as the consolidated consequence of historical orogenesis and climatic oscillations. The visualization of dispersal corridors as the function of population genetic connectivity became crucial to elucidate the spatiotemporal dynamics of organisms. However, geodiversity and physical barriers created by paleo geo-climatic events acted vigorously to impact notable alterations in the phylogeographic pattern and dispersal corridors. Therefore, to achieve detailed phylogeography, locate dispersal corridors and estimate genetic connectivity, we integrated phylogeography with species distribution modelling and least cost path of Mirabilis himalaica (Edgew.) Heimerl in the HHM. We amplified four cpDNA regions (petL-psbE, rps16-trnK, rps16 intron, trnS-trnG), and a low copy nuclear gene (G3pdh) from 241 individuals of 29 populations. SAMOVA, genealogical relationships, and phylogenetic analysis revealed four spatially structured phylogroups for M. himalaica with the onset of diversification in late Pliocene (c. 3.64 Ma). No recent demographic growth was supported by results of neutrality tests, mismatch distribution analysis and Bayesian skyline plot. Paleo-distribution modelling revealed the range dynamics of M. himalaica to be highly sensitive to geo-climatic change with limited long-distance dispersal ability and potential evolutionary adaptation. Furthermore, river drainage systems, valleys and mountain gorges were identified as the corridors for population genetic connectivity among the populations. It is concluded that recent intense mountain uplift and subsequent climatic alterations including monsoonal changes since Pliocene or early Pleistocene formulated fragmented habitats and diverse ecology that governed the habitat connectivity, evolutionary and demographic history of M. himalaica. The integrative genetic and geospatial method would bring new implications for the evolutionary process and conservation priority of HHM endemic species.

Common brain changes associated with increased activity in the forced swim test induced by drugs with different mechanisms of action

The set of ancient lakes on Sulawesi, Indonesia, represents a unique global hotspot of aquatic biodiversity. These lakes have been recognized widely because of their high number of endemic species with specialized and distinctive morphological characters, life history and ecological adaptations. An interesting case of unusual life history involving brood care exists in the planorbid limpets of the genus Protancylus, which live exclusively as epizoans on the endemic pachychilid gastropod Tylomelania. We aimed to unravel the evolutionary and phylogeographical patterns of Protancylus from the Malili lakes and Lake Poso using two mitochondrial markers in an integrated framework that includes morphological, life-history and ecological data. At least three species of Protancylus evolved allopatrically, with a newly recognized species occurring in lakes Matano and Mahalona. All species are characterized by low morphological variation, shared life-history traits including a unique reproduction strategy. Our genetic data indicates that a drift-based geographic speciation mode correlates with the present distribution pattern. The initial diversification significantly predates the ages of the respective lakes and the lineages of Protancylus are significantly older than their corresponding Tylomelania ‘hosts’. The deep split between P. pileolus of Lake Poso and the populations in the Malili lakes is remarkable and hints to a very early separation in a time frame when Sulawesi reached its current composition. As colonization and onset of diversification is strikingly different in Tylomelania and the epizoic Protancylus, co-evolutionary components in this association can be excluded and both evolved largely independently. We discuss and compare our findings to other invertebrate assemblages in the ancient lakes of Sulawesi.

Dated phylogenies and historical biogeography of Dontostemon and Clausia (Brassicaceae) mirror the palaeogeographical history of the Eurasian steppe

AbstractAimWe hypothesize that molecular signals in Eurasian steppe plants reflect their biogeographical history as well as the climate/landscape history of the Eurasian steppe. To test this hypothesis we focus here on the characteristic Eurasian steppe genera Dontostemon and Clausia (Brassicaceae), and have included all presently accepted species in our study.LocationEurasian steppe from eastern Asia to south‐eastern Europe.MethodsTo elucidate their phylogeny, we sequenced the nuclear ribosomal ITS and chloroplast trnL‐F regions. Sequence data were analysed with parsimony and Bayesian phylogenetic approaches. Divergence times were estimated using BEAST, relying on published ITS substitution rates. Distribution maps of all species of the two genera were compiled, and ancestral areas reconstructed using LAGRANGE.ResultsBoth genera originated in central and eastern Asia, with Clausia later extending its range to eastern Europe. Dated phylogenies revealed: onset of diversification in the lower and middle Miocene; evolution of the majority of groups in the upper Miocene/lower Pliocene, and further speciation events during the Quaternary. Origin and diversification within these genera coincide with the evolution and history of the modern Eurasian steppe.Main conclusionsDated phylogenies and historical biogeography of Clausia and Dontostemon mirror the climate/landscape dynamics of the steppe from its origin in the early Miocene up to the Pleistocene and Holocene.

Timing and tempo of evolutionary diversification in a biodiversity hotspot: Primulaceae on Indian Ocean islands

AbstractAimWe examined phylogenetic relationships and spatio‐temporal diversification in Indian Ocean Primulaceae, assessing correlations between speciation rates, geographical expansion and ecomorphological specialization.LocationMadagascar and Indian Ocean Islands.MethodsWe conducted phylogenetic analyses with plastid and nuclear DNA sequences of Primulaceae using maximum likelihood and Bayesian algorithms, and estimated divergence times using a Bayesian relaxed molecular clock. Temporal changes in diversification rate and possible correlations with the biogeographical history of the group were examined. We performed parametric ancestral area reconstruction incorporating a stratified palaeogeographical model that reflects changes in terrestrial configuration and the presence of phytogeographical connections through time in the western Indian Ocean Basin. Shifts in diversification rate were compared with ancestral area assignments and divergence age estimates.ResultsIndian Ocean Primulaceae were recovered as monophyletic with a sister relationship to Asian Ardisia. Oncostemum, a genus confined to Madagascar and the Comoros, was resolved as paraphyletic by the inclusion of a monophyletic Mascarene Badula group consisting of single‐island endemics. We found evidence for diversification bursts early in the history of Indian Ocean Primulaceae that correspond closely to the sequence of dispersal and the appearance of newly formed Mascarene Islands. Age estimates suggest a dispersal to Rodrigues that is older than the estimated geological age of the island.Main conclusionsResults suggest a Madagascan origin of Indian Ocean Primulaceae with subsequent dispersal to the Mascarenes in the middle to late Miocene, with initial establishment on either Mauritius or Rodrigues and subsequent stepping‐stone dispersal to the other two Mascarene islands within the last 2 Myr. Analyses suggest that diversification has slowed over time, with significant rate changes following dispersal to new geographical areas. Onset of diversification in species‐rich Oncostemum appears to have been recent, with major cladogenesis commencing in the early Pliocene.

TESTING FOR UNEQUAL RATES OF MORPHOLOGICAL DIVERSIFICATION IN THE ABSENCE OF A DETAILED PHYLOGENY: A CASE STUDY FROM CHARACIFORM FISHES

This study develops the random phylogenies rate test (RAPRATE), a likelihood method that simulates morphological evolution along randomly generated phylogenies, and uses it to determine whether a considerable difference in morphological diversity between two sister clades of South American fishes should be taken as evidence of differing rates of morphological change or lineage turnover. Despite identical ages of origin, similar species richness, and sympatric geographic distributions, the morphological and ecological diversity of the superfamily Anostomoidea exceeds that of the Curimatoidea. The test shows with 90% confidence (using variance among species as the measure of morphological diversity) or 99% confidence (using volume of occupied morphospace) that the rate of morphological change per unit time in the Anostomoidea likely exceeded that of the Curimatoidea. Variation in the rate of lineage turnover (speciation and extinction rates) is not found to affect greatly the morphological diversity of simulated clades and is not a likely explanation of the observed difference in morphological diversity in this case study. Though a 17% or greater delay in the onset of diversification in the Curimatoidea remains a possible alternative explanation of unequal morphological diversification, further simulations suggest that two clades drawn from the possible treespace of the Anostomoidea and Curimatoidea will rarely differ so greatly in the onset of diversification. Several uniquely derived morphological and ecological features of the Anostomoidea and Curimatoidea may have accelerated or decelerated their rate of morphological change, including a marked lengthening of the quadrate that may have relaxed structural constraints on the evolution of the anostomoid jaw.