Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice

Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic-scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi-arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements.

The origin and speciation of orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae)

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.

Introduced and extinct: neglected archival specimens shed new light on the historical biogeography of an iconic avian species in the Mediterranean

Collection specimens provide valuable and often overlooked biological material that enables addressing relevant, long-unanswered questions in conservation biology, historical biogeography, and other research fields. Here, we use preserved specimens to analyze the historical distribution of the black francolin (Francolinus francolinus, Phasianidae), a case that has recently aroused the interest of archeozoologists and evolutionary biologists. The black francolin currently ranges from the Eastern Mediterranean and the Middle East to the Indian subcontinent, but, at least since the Middle Ages, it also had a circum-Mediterranean distribution. The species could have persisted in Greece and the Maghreb until the 19th century, even though this possibility had been questioned due to the absence of museum specimens and scant literary evidence. Nevertheless, we identified four 200-year-old stuffed black francolins-presumably the only ones still existing-from these areas and sequenced their mitochondrial DNA control region. Based on the comparison with conspecifics (n = 396) spanning the entirety of the historic and current species range, we found that the new samples pertain to previously identified genetic groups from either the Near East or the Indian subcontinent. While disproving the former occurrence of an allegedly native westernmost subspecies, these results point toward the role of the Crown of Aragon in the circum-Mediterranean expansion of the black francolin, including the Maghreb and Greece. Genetic evidence hints at the long-distance transport of these birds along the Silk Road, probably to be traded in the commerce centers of the Eastern Mediterranean.

Reticulate evolution of the tertiary relict Osmanthus

When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.

Bayesian total-evidence dating revisits sloth phylogeny and biogeography: a cautionary tale on morphological clock analyses

Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae", whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models, and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.

Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity

The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.

Phylogenetic relationships and biogeography of Asia Callicarpa (Lamiaceae), with consideration of a long-distance dispersal across the Pacific Ocean -insights into divergence modes of pantropical flora

There are about 140 species of Callicarpa L. 1753 (Lamiaceae), with more species richness in tropical to subtropical Asia and the New World. The genus might provide an insight into the amphi-Pacific disjunction pattern of tropical and subtropical vegetation. This study has greatly improved the phylogenetic underpinning for Callicarpa, derived from more inclusive taxonomic samplings, and employing data on both two-nuclear and eight-chloroplast regions. To address time and patterns of diversification in Callicarpa, we conducted divergence time and biogeographic analyses, and inferred shifts in the distribution areas across the phylogenetic clades. Our phylogenetic results show that Callicarpa is monophyletic with respect to the groups considered, and eight well-supported primary clades were discerned in the combined analyses. Our estimates indicated that the crown group of Callicarpa originates around the Late-Eocene (ca. 36.23 Ma) and diversification within most clades is concentrated in the Miocene and continued to the Pleistocene. In addition, our biogeographic analyses suggested that the probable ancestor of the Callicarpa crown clade originated in East Asia and Southeast Asia. Multiple dispersal and vicariance events contributed to the current distribution of the taxa. Furthermore, this genus expanded eastward out of East and Southeast Asia to the New World by long-distance dispersal, which inspired us to better understand the amphi-Pacific disjunct distribution.

Changes of Cinchona distribution over the past two centuries in the northern Andes

The Cinchona genus is important for humanity due to its ethnobotanical properties, and in particular its ability to prevent and treat malaria. However, there have been historical changes of Cinchona distribution in the tropical Andes that remain undocumented. In the late eighteenth and early nineteenth centuries, several explorers recorded Cinchona precise localities in present-day Colombia and Ecuador, countries which harbour about half of the species of the genus, including C. officinalis. We compare historical and twentieth-century records to evaluate whether elevational ranges, mean elevation and latitude varied between the two periods. A large expansion of 662.5 m in average elevation for Cinchona and 792.5 m in elevational range for C. officinalis was found. These findings have implications for the conservation of economically important species and help us understand the impacts of the Anthropocene over time.

Diversity, Distribution, Systematics and Conservation Status of Podocarpaceae

Among conifer families, Podocarpaceae is the second largest, with amazing diversity and functional traits, and it is the dominant Southern Hemisphere conifer family. However, comprehensive studies on diversity, distribution, systematic and ecophysiological aspects of the Podocarpaceae are sparse. We aim to outline and evaluate the current and past diversity, distribution, systematics, ecophysiological adaptations, endemism, and conservation status of podocarps. We analyzed data on the diversity and distribution of living and extinct macrofossil taxa and combined it with genetic data to reconstruct an updated phylogeny and understand historical biogeography. Podocarpaceae today contains 20 genera and approximately 219 taxa (201 species, 2 subspecies, 14 varieties and 2 hybrids) placed in three clades, plus a paraphyletic group/grade of four distinct genera. Macrofossil records show the presence of more than 100 podocarp taxa globally, dominantly from the Eocene-Miocene. Australasia (New Caledonia, Tasmania, New Zealand, and Malesia) is the hotspot of living podocarps diversity. Podocarps also show remarkable adaptations from broad to scale leaves, fleshy seed cones, animal dispersal, shrubs to large trees, from lowland to alpine regions and rheophyte to a parasite (including the only parasitic gymnosperm-Parasitaxus) and a complex pattern of seed and leaf functional trait evolution.

Tubulosae, Inferred from Phylogenomic Data

The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.

Spatio-Temporal Evolutionary Patterns of the Pieridae Butterflies (Lepidoptera: Papilionoidea) Inferred from Mitogenomic Data

Pieridae is one of the largest and almost cosmopolitan groups of butterflies, which plays an important role in natural ecosystems; however, to date, its phylogeny and evolutionary history have not been fully resolved. In this study, we obtained the complete or nearly complete mitochondrial genomes of 100 pierid taxa (six newly sequenced, sixty extracted from the whole-genome data, and thirty-four directly available from GenBank). At the same time, for the first time, we conducted comparative mitogenomic and phylogenetic analyses based on these mitogenomic data, to further clarify their spatio-temporal evolutionary patterns. Comparative mitogenomic analysis showed that, except for cox2, the GC content of each of the 13 protein-coding genes (PCGs) in the rapidly diverging subfamily Pierinae was higher than in its sister group Coliadinae. Moreover, the dN/dS values of nine genes (atp6, atp8, cox1, cox3, cob, nad1, nad3, nad5, and nad6) in Pierinae were also relatively higher than those in its sister group, Coliadinae. Phylogenetic analysis showed that all the resultant phylogenetic trees were generally in agreement with those of previous studies. The Pierinae family contained six clades in total with the relationship of (Leptosiaini + (((Nepheroniini + Arthocharidini) + Teracolini) + (Pierini + Elodini))). The Pieridae originated in the Palearctic region approximately 72.3 million years ago in the late Cretaceous, and the subfamily Pierinae diverged from this family around 57.9 million years ago in the Oriental region, shortly after the K-Pg mass extinction event; in addition, the spatio-temporal evolutionary patterns of Pierinae were closely correlated with geological events and environmental changes, as well as the host plant coevolutionary scenario in Earth's history. However, some incongruencies were observed between our results and those of previous studies in terms of shallow phylogenies for a few taxa, and should be further investigated.

Historical Biogeography of Earwigs

The Dermaptera are an insect order exhibiting their highest diversity in the tropical areas of the southern hemisphere. This pattern has been considered a reflection of a Gondwanan origin. However, this hypothesis has not been tested through analytical methods. In this paper, the world distribution of earwigs was analysed by using the 'Cladistic Analysis of Distributions and Endemism' (CADE), a method which groups areas of endemism on the basis of shared distributions and phylogenetic relationships among taxa. In addition, clustering techniques were applied to depict biotic relationships based on similarity indices. Results of CADE support the idea that Gondwanan fragmentation exerted a crucial role in shaping the current distribution of the main clades of earwigs. However, the relationships between India with South East Asia suggested a biotic interchange occurred after the Indian collision with the Eurasian plate. The overall scenario emerging from cluster analyses revealed a strong influence of dispersal events. Overall, the distribution of earwig major clades indicates that their biogeographical history was mainly characterized by vicariance events (led by the break-up of Gondwana) followed by large scale dispersal processes constrained by the Himalayan orogenesis and the presence of colder temperatures, which have largely hampered the colonization of the northern hemisphere.

Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family

PREMISE

The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres.

METHODS

We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification.

RESULTS

Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas.

CONCLUSIONS

Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.

Plant migration under long-lasting hyperaridity - phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth

The post-Miocene climatic histories of arid environments have been identified as key drivers of dispersal and diversification. Here, we investigate how climatic history correlates with the historical biogeography of the Atacama Desert genus Cristaria (Malvaceae). We analyze phylogenetic relationships and historical biogeography by using next-generation sequencing (NGS), molecular clock dating, Dispersal Extinction Cladogenesis and Bayesian sampling approaches. We employ a novel way to identify biogeographically meaningful regions as well as a rarely utilized program permitting the use of dozens of ancestral areas. Partial incongruence between the established taxonomy and our phylogenetic data argue for a complex historical biogeography with repeated introgression and incomplete lineage sorting. Cristaria originated in the central southern part of the Atacama Desert, from there the genus colonized other areas from the late Miocene onwards. The more recently diverged lineages appear to have colonized different habitats in the Atacama Desert during pluvial phases of the Pliocene and early Pleistocene. We show that NGS combined with near-comprehensive sampling can provide an unprecedented degree of phylogenetic resolution and help to correlate the historical biogeography of plant communities with cycles of arid and pluvial phases.

Molecular phylogeny reveals the past transoceanic voyages of drywood termites (Isoptera, Kalotermitidae)

Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ∼120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Ma (75–93 Ma 95% highest posterior density), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ∼40 disjunctions among biogeographic realms were dated at <50 Ma, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

Phylogenomics and continental biogeographic disjunctions: insight from the Australian starflowers (Calytrix)

PREMISE

Continental-scale disjunctions and associated drivers are core research interests in biogeographic studies. Here, we selected a species-rich Australian plant genus (Calytrix; Myrtaceae) as a case study to investigate these patterns. Species of this endemic Australian starflower genus have a disjunct distribution across the mesic fringes of the continent and are largely absent from the arid center.

METHODS

We used high-throughput sequencing to generate unprecedented resolution and near complete species-level nuclear and plastid phylogenies for Calytrix. BioGeoBEARS and biogeographic stochastic mapping were used to infer ancestral areas, the relative contributions of vicariance and dispersal events, and directionality of dispersal.

RESULTS

Present-day disjunctions in Calytrix are explained by a combination of scenarios: (1) retreat of multiple lineages from the continental center to the more mesic fringes as Australia became progressively more arid, with subsequent extinction in the center as well as (2) origination of ancestral lineages in southwestern Australia (SWA) for species-rich clades. The SWA biodiversity hotspot is a major diversification center and the most common source area of dispersals, with multiple lineages originating in SWA and subsequently spreading to the adjacent arid Eremaean region.

CONCLUSIONS

Our results suggest that major extinction, as a result of cooling and drying of the Australian continent in the Eocene-Miocene, shaped the present-day biogeography of Calytrix. We hypothesize that this peripheral vicariance pattern, which is similar to the African Rand flora, may explain the disjunctions of many other Australian plant groups. Further studies with densely sampled phylogenies are required to test this hypothesis.

The evolutionary history of an accidental model organism, the leopard gecko Eublepharis macularius (Squamata: Eublepharidae)

The leopard gecko, Eublepharis macularius, is a widely used model organism in laboratory and experimental studies. The high phenotypic diversity in the pet trade, the fact that the provenance of different breeding lines is unknown, and that distinct Eublepharis species are known to hybridize, implies that the continued use of E. macularius as a model requires clarity on the origin of the lineages in the pet trade. We combine multi-locus sequence data and the first range-wide sampling of the genus Eublepharis to reconstruct the evolutionary history of the Eublepharidae and Eublepharis, with an updated time-tree for the Eublepharidae. Our sampling includes five of the six recognized species and additional nominal taxa of uncertain status comprising 43 samples from 34 localities plus 48 pet-trade samples. The Eublepharidae began diversifying in the Cretaceous. Eublepharis split from its sister genera in Africa in the Palaeocene-Eocene, and began diversifying in the Oligocene-Miocene, with late Miocene-Pliocene cladogenesis giving rise to extant species. The current species diversity within this group is moderately underestimated. Our species delimitation suggests 10 species with four potentially unnamed divergent lineages in Iran, India and Pakistan. All 30 individuals of E. macularius that we sampled from the pet trade, which include diverse morphotypes, come from a few shallow E. macularius clades, confirming that lab and pet trade strains are part of a single taxon. One of the wild-caught haplotypes of E. macularius, from near Karachi, Pakistan, is identical to (10) pet-trade samples and all other captive populations are closely related to wild-caught animals from central/southern Pakistan (0.1-0.5 % minimum pairwise uncorrected ND2 sequence divergence).

Historical biogeographical analysis of the Udoteaceae (Bryopsidales, Chlorophyta) elucidates origins of high species diversity in the Central Indo-Pacific, Western Indian Ocean and Greater Caribbean regions

There is a growing interest in elucidating the biogeographical processes underlying biodiversity patterns of seaweeds, with recent studies largely focusing on red and brown macroalgae. This study focuses on the siphonous green algal family Udoteaceae, which is diverse and globally distributed in tropical to warm-temperate seas, and includes species that form important components of tropical reefs. We explored the historical processes that have shaped current biodiversity patterns in the family by analyzing a comprehensive dataset of 568 specimens sampled across its geographical range, and including 45 species, corresponding to 59% of the known diversity. Historical biogeographical analysis was based on a three-locus time-calibrated phylogeny, and probabilistic modeling of geographical range evolution. Many species were found to have restricted ranges, indicative of low dispersal capacity. Our analysis points toward a Western Tethys origin and early diversification of the Udoteaceae in the Triassic period. Three centers of diversity were identified, which are, in order of highest species richness, the Central Indo-Pacific, the Western Indian Ocean, and the Greater Caribbean. Different drivers have likely played a role in shaping these diversity centres. Species richness in the Central Indo-Pacific likely resulted from speciation within the region, as well as recolonization from neighbouring regions, and overlap of some wider ranged species, corroborating the "biodiversity feedback" model. Species richness in the Western Indian Ocean can be explained by ancient and more recent diversification within the region, and dispersal from the Central Indo-Pacific. The Greater Caribbean region was colonized more recently, followed by diversification within the region.

Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences

The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.

Extended phylogeography of the ancestral Morchella anatolica supports preglacial presence in Europe and Mediterranean origin of morels

Over 80 species are recognized in the commercially important genus Morchella, many of them endemic to specific regions or continents. Among them, M. anatolica and M. rufobrunnea are the earliest diverging lineages and are key in decoding the evolutionary history, global biogeography, and ecological trends within this iconic genus. Early ancestral area reconstruction (AAR) tests postulated a western North American origin of morels but had not included in the analyses M. anatolica, whose phylogenetic identity remained at the time unresolved. Following new collections of M. anatolica and M. rufobrunnea from the Mediterranean islands of Cyprus, Kefalonia, Lesvos, Malta, and Zakynthos, we performed revised AAR tests to update the historical biogeography of the genus. Our results, inferred from multilocus analysis of an expanded data set of 79 phylospecies, challenge previous reconstructions and designate the Mediterranean basin as the most likely place of origin for morels. Detailed morphoanatomical analyses demonstrate that ascocarp rufescence, the nondarkening apothecial ridges, the absence of a sinus, and the stipe pruinescence are all stable synapomorphic features of sect. Rufobrunnea, which could be interpreted as ancestral for the genus. The saprotrophic mode of nutrition, suggested by the prolific in vitro growth of M. anatolica, might also be an ancestral trait. Emended descriptions, including extensive imagery and scanning electron microscopy, are provided, and a new evolutionary hypothesis of the genus is proposed.

Phylogeny and historical biogeography analysis support Caucasian and Mediterranean centres of origin of key holoparasitic Orobancheae (Orobanchaceae) lineages

The extensive diversity of the tribe Orobancheae, the most species-rich lineage of holoparasitic Orobanchaceae, is concentrated in the Caucasus and Mediterranean regions of the Old World. This extant diversity has inspired hypotheses that these regions are also centres of origin of its key lineages, however the ability to test hypotheses has been limited by a lack of sampling and phylogenetic information about the species, especially in the Caucasus region. First, we assessed the phylogenetic relationships of several poorly known, problematic, or newly described species and host-races of four genera of Orobancheae occurring in the Caucasus region-Cistanche, Phelypaea, Phelipanche and Orobanche-using nuclear ribosomal (ITS) and plastid (trnL-trnF) sequence data. Then we applied a probablistic dispersal-extinction-cladogenesis model of historical biogeography across a more inclusive clade of holoparasites, to explicitly test hypotheses of Orobancheae diversification and historical biogeography shifts. In sum, we sampled 548 sequences (including 196 newly generated) from 13 genera, 140 species, and 175 taxa across 44 countries. We find that the Western Asia (particularly the Caucasus) and the Mediterranean are the centre of origin for large clades of holoparasitic Orobancheae within the last 6 million years. In the Caucasus, the centres of diversity are composed both of long-branch taxa and shallow, recently diversified clades, while Orobancheae diversity in the Mediterranean appears to represent mainly recent diversification.

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.

Environmental differences are correlated with the distribution pattern of cytotypes in Veronica subsection Pentasepalae at a broad scale

BACKGROUND AND AIMS

The distribution of cytotypes and its potential correlation with environmental variables represent a cornerstone to understanding the origin and maintenance of polyploid lineages. Although many studies have addressed this question in single species at a regional scale, only a few have attempted to decipher this enigma in groups of closely related species at a broad intercontinental geographical scale. Here, we consider approx. 20 species of a diploid-polyploid complex (Veronica subsect. Pentasepalae) of recent and rapid diversification represented in Europe and North Africa to study the frequency and distribution of cytotypes and their relationship to environmental variables.

METHODS

A total of 680 individuals (207 populations) were sampled. Ploidy levels were determined using flow cytometry. Ecological differentiation among cytotypes was tested using climatic and environmental variables related to temperature, precipitation, vegetation and biogeographical region, among others, and by performing univariate and multivariate (constrained principal coordinates analysis) analyses.

KEY RESULTS

Four ploidy levels (2x, 4x, 6x and 8x) were found and genome downsizing was observed to occur within the group. Plants of different ploidy level are ecologically differentiated, with hexaploids and octoploids occurring in wetter and colder habitats with a higher seasonality than diploids. A south to north distribution pattern was found, with diploids occupying southern refugial areas and octoploids being more frequent in northern regions of Europe above the permafrost boundary.

CONCLUSIONS

The distribution of cytotypes can be explained by ecological differentiation, the geographical position of refuge areas during the Quaternary climatic oscillations as well as by ice and permafrost retreat patterns. The Balkan Peninsula constitutes the most important contact zone between cytotypes. This work provides the first comprehensive ploidy screening within V. subsect. Pentasepalae at a broad scale and indicates that polyploidy and genome downsizing might have contributed to the colonization of new habitats in a recently diverged polyploid complex.

Global predictors of alien plant establishment success: combining niche and trait proxies

Biological invasions are on the rise globally. To reduce future invasions, it is imperative to determine the naturalization potential of species. Until now, screening approaches have relied largely on species-specific functional feature data. Such information is, however, time-consuming and expensive to collect, thwarting the screening of large numbers of potential invaders. We propose to resolve such data limitations by developing indicators of establishment success of alien species that can be readily derived from open-access databases. These indicators describe key features of successfully established aliens, including estimates of potential range size, niche overlap with human-disturbed environments, and proxies of species traits related to their palaeoinvasions and local dominance capacities. We demonstrate the utility of this new approach by applying it to two large and highly invasive plant groups: Australian acacias and eucalypts. Our results show that these indicators robustly predict establishment successes and failures in each clade independently, and that they can cross-predict establishment in these two clades. Interestingly, the indicator identified as most important was species potential range size on Earth, a variable too rarely considered as a predictor. By successfully identifying key features that predispose Australian plants to naturalize, we provide an objective and cost-effective protocol for flagging high-risk introductions.

A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes)

The evolution of pantropically distributed clades has puzzled palaeo- and neontologists for decades regarding the different hypotheses about where they originated. In this study, we explored how a pantropical distribution arose in a diverse clade with a rich fossil history: the avian order Coraciiformes. This group has played a central role in the debate of the biogeographical history of Neoaves. However, the order lacked a coherent species tree to inform study of its evolutionary dynamics. Here, we present the first complete species tree of Coraciiformes, produced with 4858 ultraconserved elements, which supports two clades: (1) Old World-restricted bee-eaters, rollers and ground-rollers; and (2) New World todies and motmots, and cosmopolitan kingfishers. Our results indicated two pulses of diversification: (1) major lineages of Coraciiformes arose in Laurasia approximately 57 Ma, followed by independent dispersals into equatorial regions, possibly due to tracking tropical habitat into the lower latitudes-the Coracii (Coraciidae + Brachypteraciidae) into the Afrotropics, bee-eaters throughout the Old World tropics, and kingfishers into the Australasian tropics; and (2) diversification of genera in the tropics during the Miocene and Pliocene. Our study supports the important role of Laurasia as the geographical origin of a major pantropical lineage and provides a new framework for comparative analyses in this charismatic bird radiation.

Pleistocene climate change and the formation of regional species pools

Although the description of bioregions dates back to the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We used a network approach to identify regional and sub-regional faunas of European Carabus beetles and developed a method to explore the relative contribution of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at the Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration of Carabus faunas occurred during the Pleistocene. Our results show how extreme recent historical events-such as Pleistocene climate cooling, rather than just deep-time evolutionary processes-can profoundly modify the composition and structure of geographical species pools.

Climatic shifts drove major contractions in avian latitudinal distributions throughout the Cenozoic

Many higher level avian clades are restricted to Earth's lower latitudes, leading to historical biogeographic reconstructions favoring a Gondwanan origin of crown birds and numerous deep subclades. However, several such "tropical-restricted" clades (TRCs) are represented by stem-lineage fossils well outside the ranges of their closest living relatives, often on northern continents. To assess the drivers of these geographic disjunctions, we combined ecological niche modeling, paleoclimate models, and the early Cenozoic fossil record to examine the influence of climatic change on avian geographic distributions over the last ∼56 million years. By modeling the distribution of suitable habitable area through time, we illustrate that most Paleogene fossil-bearing localities would have been suitable for occupancy by extant TRC representatives when their stem-lineage fossils were deposited. Potentially suitable habitat for these TRCs is inferred to have become progressively restricted toward the tropics throughout the Cenozoic, culminating in relatively narrow circumtropical distributions in the present day. Our results are consistent with coarse-scale niche conservatism at the clade level and support a scenario whereby climate change over geological timescales has largely dictated the geographic distributions of many major avian clades. The distinctive modern bias toward high avian diversity at tropical latitudes for most hierarchical taxonomic levels may therefore represent a relatively recent phenomenon, overprinting a complex biogeographic history of dramatic geographic range shifts driven by Earth's changing climate, variable persistence, and intercontinental dispersal. Earth's current climatic trajectory portends a return to a megathermal state, which may dramatically influence the geographic distributions of many range-restricted extant clades.

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

PREMISE OF THE STUDY

A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia.

METHODS

A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared.

KEY RESULTS

A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade.

CONCLUSIONS

Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

PREMISE OF THE STUDY

A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia.

METHODS

A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared.

KEY RESULTS

A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade.

CONCLUSIONS

Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Molecular Phylogeny and Historical Biogeography of the Butterfly Tribe Aeromachini Tutt (Lepidoptera: Hesperiidae) from China

: The butterfly tribe Aeromachini Tutt, 1906 is a large group of skippers. In this study, a total of 10 genera and 45 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2093 bp). The combined dataset was analyzed with maximum likelihood inference using IQtree. We found strong support for monophyly of Aeromachini from China and support for the most recent accepted species in the tribe. Two paraphyletic genera within Aeromachini are presented and discussed. The divergence time estimates with BEAST and ancestral-area reconstructions with RASP provide a detailed description about the historical biogeography of the Aeromachini from China. The tribe very likely originated from the Hengduan Mountains in the late Ecocene and expanded to the Himalaya Mountains and Central China Regions. A dispersal-vicariance analysis suggests that dispersal events have played essential roles in the distribution of extant species, and geological and climatic changes have been important factors driving current distribution patterns.

No borders during the post-glacial assembly of European bryophytes

Climatic fluctuations during the Last Glacial Maximum (LGM) exerted a profound influence on biodiversity patterns, but their impact on bryophytes, the second most diverse group of land plants, has been poorly documented. Approximate Bayesian computations based on coalescent simulations showed that the post-glacial assembly of European bryophytes involves a complex history from multiple sources. The contribution of allochthonous migrants was 95-100% of expanding populations in about half of the 15 investigated species, which is consistent with the globally balanced genetic diversities and extremely low divergence observed among biogeographical regions. Such a substantial contribution of allochthonous migrants in the post-glacial assembly of Europe is unparalleled in other plants and animals. The limited role of northern micro-refugia, which was unexpected based on bryophyte life-history traits, and of southern refugia, is consistent with recent palaeontological evidence that LGM climates in Eurasia were much colder and drier than what palaeoclimatic models predict.

Evolution of population structure in an estuarine-dependent marine fish

Restriction site-associated DNA (RAD) sequencing was used to characterize neutral and adaptive genetic variation among geographic samples of red drum, Sciaenops ocellatus, an estuarine-dependent fish found in coastal waters along the southeastern coast of the United States (Atlantic) and the northern Gulf of Mexico (Gulf). Analyses of neutral and outlier loci revealed three genetically distinct regional clusters: one in the Atlantic and two in the northern Gulf. Divergence in neutral loci indicated gradual genetic change and followed a linear pattern of isolation by distance. Divergence in outlier loci was at least an order of magnitude greater than divergence in neutral loci, and divergence between the regions in the Gulf was twice that of divergence between other regions. Discordance in patterns of genetic divergence between outlier and neutral loci is consistent with the hypothesis that the former reflects adaptive responses to environmental factors that vary on regional scales, while the latter largely reflects drift processes. Differences in basic habitat, initiated by glacial retreat and perpetuated by contemporary oceanic and atmospheric forces interacting with the geomorphology of the northern Gulf, followed by selection, appear to have led to reduced gene flow among red drum across the northern Gulf, reinforcing differences accrued during isolation and resulting in continued divergence across the genome. This same dynamic also may pertain to other coastal or nearshore fishes (18 species in 14 families) where genetically or morphologically defined sister taxa occur in the three regions.

Molecular phylogenetics and historical biogeography of the tribe Lilieae (Liliaceae): bi-directional dispersal between biodiversity hotspots in Eurasia

Background and Aims

The role played by the Qinghai-Tibet Plateau (QTP) in the organismal diversification and biogeography of plants in the Northern Hemisphere has attracted much attention from evolutionary biologists. Here we use tribe Lilieae (Liliaceae), including primarily temperate and alpine lineages with disjunct distributions in the North Temperate Zone, as a case study to shed light upon these processes.

Methods

Using 191 taxa (five outgroup taxa) comprising more than 60 % of extant Lilieae species across the entire geographical range, we analyse phylogenetic relationships based on three plastid markers (matK, rbcL, rpl16) and nuclear ITS. Divergence time estimation and ancestral range reconstruction were further inferred.

Key Results

The results support a monophyletic Lilieae divided into four clades. Lilium is nested within Fritillaria, which is paraphyletic and partitioned into two clades, New World and Old World, in the chloroplast DNA (cpDNA) analysis. Incongruences between the ITS and cpDNA trees may be explained by divergent ITS paralogues and hybridization. Lilieae originated around 40-49 (28-67) Mya and probably diversified in the QTP region with four major clades that were established during the Oligocene and the Early Miocene. Uplift of the QTP and climatic changes probably drove early diversification of Lilieae in the QTP region. A rapid radiation occurred during the Late Miocene and the Pleistocene, coinciding temporally with recent orogenic process in the QTP region and climatic oscillations. Several lineages dispersed out of the QTP.

Conclusions

Lineage persistence and explosive radiation were important processes for establishing high species diversity of Lilieae in the QTP region. Both long-distance dispersal and migration across Beringia probably contributed to the modern distribution range of Lilieae. Our study shows that biotic interchanges between the QTP region and Irano-Turanian region and the Mediterranean Basin were bi-directional, suggesting the latter was a secondary centre of diversity.

Explaining the ocean's richest biodiversity hotspot and global patterns of fish diversity

For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3-34 million years ago. These relatively old colonizations allowed more time for richness to build up through in situ diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates.

Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east-west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east-west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe. This clade has had a challenging taxonomic history, but the current classification consists of ~77 species in three families, the Travuniidae, Paranonychidae, and Nippononychidae. Travunioidea classification has traditionally been based on structure of the tarsal claws of the hind legs. However, it is now clear that tarsal claw structure is a poor taxonomic character due to homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived from capture of ultraconserved elements (UCEs) to reconstruct travunioid relationships. Data matrices consisting of 317-677 loci were used in maximum likelihood, Bayesian, and species tree analyses. Resulting phylogenies recover four consistent and highly supported clades; the phylogenetic position and taxonomic status of the enigmatic genus Yuria is less certain. Based on the resulting phylogenies, a revision of Travunioidea is proposed, now consisting of the Travuniidae, Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the new family Cryptomastridae Derkarabetian & Hedin, fam. n., diagnosed here. The phylogenetic utility and diagnostic features of the intestinal complex and male genitalia are discussed in light of phylogenomic results, and the inappropriateness of the tarsal claw in diagnosing higher-level taxa is further corroborated.

Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models

The development of process-based probabilistic models for historical biogeography has transformed the field by grounding it in modern statistical hypothesis testing. However, most of these models abstract away biological differences, reducing species to interchangeable lineages. We present here the case for reintegration of biology into probabilistic historical biogeographical models, allowing a broader range of questions about biogeographical processes beyond ancestral range estimation or simple correlation between a trait and a distribution pattern, as well as allowing us to assess how inferences about ancestral ranges themselves might be impacted by differential biological traits. We show how new approaches to inference might cope with the computational challenges resulting from the increased complexity of these trait-based historical biogeographical models.

Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira)

Pleurodires or side-necked turtles are today restricted to freshwater environments of South America, Africa-Madagascar and Australia, but in the past they were distributed much more broadly, being found also on Eurasia, India and North America, and marine environments. Two hypotheses were proposed to explain this distribution; in the first, vicariance would have shaped the current geographical distribution and, in the second, extinctions constrained a previously widespread distribution. Here, we aim to reconstruct pleurodiran biogeographic history and diversification patterns based on a new phylogenetic hypothesis recovered from the analysis of the largest morphological dataset yet compiled for the lineage, testing which biogeographical process prevailed during its evolutionary history. The resulting topology generally agrees with previous hypotheses of the group and shows that most diversification shifts were related to the exploration of new niches, e.g. littoral or marine radiations. In addition, as other turtles, pleurodires do not seem to have been much affected by either the Cretaceous-Palaeogene or the Eocene-Oligocene mass extinctions. The biogeographic analyses highlight the predominance of both anagenetic and cladogenetic dispersal events and support the importance of transoceanic dispersals as a more common driver of area changes than previously thought, agreeing with previous studies with other non-turtle lineages.

A signature of dynamic biogeography: enclaves indicate past species replacement

Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future.

Riders in the sky (islands): using a mega-phylogenetic approach to understand plant species distribution and coexistence at the altitudinal limits of angiosperm plant life

AIM

Plants occurring on high-alpine summits are generally expected to persist due to adaptations to extreme selective forces caused by the harshest climates where angiosperm life is known to thrive. We assessed the relative effects of this strong environmental filter and of other historical and stochastic factors driving plant community structure in very high-alpine conditions (up to 4,000m).

LOCATION

European Alps, Écrins National Park, France.

METHODS

Using species occurrence data collected from floristic surveys on 15 summits (2,791 m - 4,102 m a.s.l.) throughout the Écrins range, along with existing molecular sequence data obtained from GenBank, we used a mega-phylogenetic approach to evaluate the phylogenetic structure of high-alpine plant species assemblages. We used three nested species pools and two null models to address the importance of species-specific and species-neutral processes for driving coexistence.

RESULTS

Compared to the entire species pool of the study region, alpine summits exhibited a strong signal of phylogenetic clustering. Restricting statistical sampling to environmentally and historically defined species pools reduced the significance of this pattern. However, we could not reject a model that explicitly incorporates neutral colonization and local extinction in shaping community structure for dominant plant orders. Between summits, phylogenetic turnover was generally lower than expected. Environmental drivers did not explain overall phylogenetic patterns, but we found significant geographic and climatic structure in phylogenetic diversity at finer taxonomic scales.

MAIN CONCLUSIONS

Although we found evidence for strong phylogenetic clustering within alpine summits, we were not able to reject models of species-neutral processes to explain patterns of floristic diversity. Our results suggest that plant community structure in high-alpine regions can also be shaped by neutral processes, and not through the sole action of environmental selection as traditionally assumed for harsh and stressful environments.

Historical relationships of areas of endemism of the Brazilian Atlantic rain forest: a cladistic biogeographic analysis of harvestman taxa (Arachnida: Opiliones)

Based on a cladistic biogeographic analysis of 6 species-level phylogenies of harvestman taxa, we searched for congruence in the historical relationships of 12 areas of endemism of the Brazilian Atlantic Rain Forest. We constructed general area cladograms using Primary Brooks Parsimony Analysis (BPA), BPA of nodes, and paralogy-free subtree analysis. These analyses resulted in 6 general area cladograms, that allow to infer a general pattern of the relationships among areas of endemism from the Brazilian Atlantic Rain Forest. Northern areas resulted related basally showing main disjunctions at the Doce River Valley and Todos os Santos Bay/São Francisco River Valley. The remaining areas of endemism were included in a southern and a southeastern block, separated by the Ribeira do Iguape Valley. Incongruence Length Differences tests showed no significant incongruence among the resulting cladograms and other matrix partitions. We concluded that tectonism and ancient marine transgressions were the probable processes responsible for the main disjunctions, whereas Neogene refugia seem to have caused the more recent disjunctions. The general pattern and redundancy in area relationships suggest a model of main reiterative barriers in diversification at multiple times for the evolution of the Atlantic Rain Forest. The renewal of cladistic biogeography and the search for common biogeographic patterns are discussed.

Mitochondrial Phylogenomics Resolves the Global Spread of Higher Termites, Ecosystem Engineers of the Tropics

The higher termites (Termitidae) are keystone species and ecosystem engineers. They have exceptional biomass and play important roles in decomposition of dead plant matter, in soil manipulation, and as the primary food for many animals, especially in the tropics. Higher termites are most diverse in rainforests, with estimated origins in the late Eocene (∼54 Ma), postdating the breakup of Pangaea and Gondwana when most continents became separated. Since termites are poor fliers, their origin and spread across the globe requires alternative explanation. Here, we show that higher termites originated 42-54 Ma in Africa and subsequently underwent at least 24 dispersal events between the continents in two main periods. Using phylogenetic analyses of mitochondrial genomes from 415 species, including all higher termite taxonomic and feeding groups, we inferred 10 dispersal events to South America and Asia 35-23 Ma, coinciding with the sharp decrease in global temperature, sea level, and rainforest cover in the Oligocene. After global temperatures increased, 23-5 Ma, there was only one more dispersal to South America but 11 to Asia and Australia, and one dispersal back to Africa. Most of these dispersal events were transoceanic and might have occurred via floating logs. The spread of higher termites across oceans was helped by the novel ecological opportunities brought about by environmental and ecosystem change, and led termites to become one of the few insect groups with specialized mammal predators. This has parallels with modern invasive species that have been able to thrive in human-impacted ecosystems.

DISPERSAL, VICARIANCE, AND CLOCKS: HISTORICAL BIOGEOGRAPHY AND SPECIATION IN A COSMOPOLITAN PASSERINE GENUS (ANTHUS: MOTACILLIDAE)

Dispersal and vicariant hypotheses have for decades been at odds with each other, notwithstanding the fact that both are well-established natural processes with important histories in biogeographic analyses. Despite their importance, neither dispersal nor vicariant methodologies are problem-free. The now widely used molecular techniques for generating phylogenies have provided a mechanism by which both dispersal- and vicariance-driven speciation can be better tested via the application of molecular clocks; unfortunately, substantial problems can also exist in the employment of those clocks. To begin to assess the relative roles of dispersal and vicariance in the establishment of avifaunas, especially intercontinental avifaunas, I applied a test for clocklike behavior in molecular data, as well as a program that infers ancestral areas and dispersal events, to a phylogeny of a speciose, cosmopolitan avian genus (Anthus; Motacillidae). Daughter-lineages above just 25 of 40 nodes in the Anthus phylogeny are evolving in a clocklike manner and are thus dateable by a molecular clock. Dating the applicable nodes suggests that Anthus arose nearly 7 million yr ago, probably in eastern Asia, and that between 6 and 5 million yr ago, Anthus species were present in Africa, the Palearctic, and North and South America. Speciation rates have been high throughout the Pliocene and quite low during the Pleistocene; further evidence that the Pleistocene may have had little effect in generating modern species. Intercontinental movements since 5 million yr ago have been few and largely restricted to interchange between Eurasia and Africa. Species swarms on North America, Africa, and Eurasia (but not South America or Australia) are the product of multiple invasions, rather than being solely the result of within-continent speciation. Dispersal has clearly played an important role in the distribution of this group.

HISTORICAL DIVERSIFICATION OF BIRDS IN NORTHWESTERN SOUTH AMERICA: A MOLECULAR PERSPECTIVE ON THE ROLE OF VICARIANT EVENTS

Studies of South American biodiversity have identified several areas of endemism that may have enhanced historical diversification of South American organisms. Hypotheses concerning the derivation of birds in the Chocó area of endemism in northwestern South America were evaluated using protein electrophoretic data from 14 taxonomically diverse species groups of birds. Nine of these groups demonstrated that the Chocó area of endemism has a closer historical relationship to Central America than to Amazonia, a result that is consistent with phytogeographic evidence. Within species groups, genetic distances between cis-Andean (east of the Andes) and trans-Andean (west of the Andes) taxa are, on average, roughly twice that between Chocó and Central American taxa. The genetic data are consistent with the hypotheses that the divergence of most cis-Andean and trans-Andean taxa was the result of either the Andean uplift fragmenting a once continuous Amazonian-Pacific population (Andean Uplift Hypothesis), the isolation of the two faunas in forest refugia on opposite sides of the Andes during arid climates (Forest Refugia Hypothesis), or dispersal of Amazonian forms directly across the Andes into the trans-Andean region (Across-Andes Dispersal Hypothesis). Disentangling these hypotheses is difficult due to the complexity of the Andean uplift and to the scant geologic and paleoclimatic information that elucidates diversification events in northwestern South America. Regarding the divergence of cis- and trans-Andean taxa, the genetic, geologic, and paleoclimatic data allow weak rejection of the Andean Uplift Hypothesis and weak support for the Forest Refugia and Andean Dispersal Hypotheses. The subsequent diversification of Chocó and Central American taxa was the result of Pleistocene forest refugia, marine transgressions, or parapatric speciation.

HISTORICAL BIOGEOGRAPHY OF THE BANANAQUIT (COEREBA FLAVEOLA) IN THE CARIBBEAN REGION: A MITOCHONDRIAL DNA ASSESSMENT

We analyzed mitochondrial DNA (mtDNA) restriction-site variation in bananaquit (Coereba flaveola; Aves, Coerebinae) populations sampled on 12 Caribbean islands and at 5 continental localities in Central America and northern South America. Multiple fixed restriction-site differences genetically defined several regional bananaquit populations. An mtDNA clade representing all Jamaican bananaquits was the most divergent; the estimated average sequence divergence (d_xy ) between Jamaican and all other mtDNA haplotypes surveyed was 0.027. Three groups of populations, representing Central America, northern South America, and the eastern Antilles (Puerto Rico to Grenada) were nearly equally differentiated among themselves (average d_xy = 0.014), and may represent a single, recent range expansion. Within the eastern Antilles, three geographically restricted haplotype groups were identified: Puerto Rico, north-central Lesser Antilles (U.S. Virgin Islands to St. Lucia), and Grenada-St. Vincent. The evolutionary relationships of these groups were not clear. Genetic homogeneity of the island populations from the U.S. Virgin Islands to St. Lucia suggested a recent spread of a specific north-central Lesser Antillean haplotype through most of those islands. Haplotype variation across this region indicated that this spread may have occurred in two waves, first through the southernmost islands of St. Lucia, Martinique, and Dominica, and more recently from Guadeloupe to the north. The geographic distribution of mtDNA haplotypes, and of bananaquit populations, suggests periods of invasiveness followed by relative geographic quiescence. Although most genetic studies of bird populations have revealed homogeneity over large geographic areas, our findings provide a remarkable counterexample of strong geographic structuring of mtDNA variation over relatively small distances. Furthermore, although the mtDNA data were consistent with several subspecific distinctions, it was clear that named subspecies do not define equally differentiated evolutionary entities.

Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris)

PREMISE OF THE STUDY

Our goal was to infer the phylogenetic relationships and historical biogeography of the genus Dryopteris with a focus on taxa in sub-Saharan Africa and neighboring islands. In general, little is known about the relationships between African fern species and their congeners in other geographic regions, and our aim was to determine whether the sub-Saharan African species of Dryopteris are monophyletic and evolved within Africa or arrived there via repeated dispersals into Africa from other regions.

METHODS

We obtained sequence data for five chloroplast markers from 214 species of Dryopteris and 18 outgroups. We performed phylogenetic and molecular dating analyses using a Bayesian relaxed clock method in BEAST with fossil and secondary calibration points and estimated ancestral ranges for the genus globally by comparing multiple models in BioGeoBEARS.

KEY RESULTS

We found that 22 of 27 accessions of sub-Saharan African Dryopteris belong to a large clade of 31 accessions that also includes taxa from Indian and Atlantic Ocean islands. Additional accessions of taxa from our regions of interest have Asian, Hawaiian, European, or North American species as their closest relatives.

CONCLUSIONS

The majority of sub-Saharan African Dryopteris species are descended from a shared common ancestor that dispersed to Africa from Asia approximately 10 Ma. There have been subsequent dispersal events from the African mainland to islands in the Atlantic and Indian Oceans, including Madagascar. Several additional species are estimated to have descended from ancestors that reached Africa via separate events over the last roughly 20 million years.

Out of Borneo: biogeography, phylogeny and divergence date estimates of Artocarpus (Moraceae)

BACKGROUND AND AIMS

The breadfruit genus ( Artocarpus , Moraceae) includes valuable underutilized fruit tree crops with a centre of diversity in Southeast Asia. It belongs to the monophyletic tribe Artocarpeae, whose only other members include two small neotropical genera. This study aimed to reconstruct the phylogeny, estimate divergence dates and infer ancestral ranges of Artocarpeae, especially Artocarpus , to better understand spatial and temporal evolutionary relationships and dispersal patterns in a geologically complex region.

METHODS

To investigate the phylogeny and biogeography of Artocarpeae, this study used Bayesian and maximum likelihood approaches to analyze DNA sequences from six plastid and two nuclear regions from 75% of Artocarpus species, both neotropical Artocarpeae genera, and members of all other Moraceae tribes. Six fossil-based calibrations within the Moraceae family were used to infer divergence times. Ancestral areas and estimated dispersal events were also inferred.

KEY RESULTS

Artocarpeae, Artocarpus and four monophyletic Artocarpus subgenera were well supported. A late Cretaceous origin of the Artocarpeae tribe in the Americas is inferred, followed by Eocene radiation of Artocarpus in Asia, with the greatest diversification occurring during the Miocene. Borneo is reconstructed as the ancestral range of Artocarpus , with dozens of independent in situ diversification events inferred there, as well as dispersal events to other regions of Southeast Asia. Dispersal pathways of Artocarpus and its ancestors are proposed.

CONCLUSIONS

Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions. The greatest amount of diversification is inferred to have occurred during the Miocene, when sea levels fluctuated and land connections frequently existed between Borneo, mainland Asia, Sumatra and Java. Many species found in these areas have extant overlapping ranges, suggesting that sympatric speciation may have occurred. By contrast, Artocarpus diversity east of Borneo (where many of the islands have no historical connections to the landmasses of the Sunda and Sahul shelves) is unique and probably the product of over water long-distance dispersal events and subsequent diversification in allopatry. This work represents the most comprehensive Artocarpus phylogeny and biogeography study to date and supports Borneo as an evolutionary biodiversity hotspot.