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opencc-zeroDec 2014View details →

Data from: Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific

A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from one another in the early Pliocene–late Miocene (c. 4.5–7.7 Ma). The remarkably deep divergences, both within and between lineages, appear to have resulted from ancient isolations, accelerated by random drift and limited genetic exchange between regions. The disjunct distributions of lineages A and C along the coasts of Japan may reflect divergence during isolation in scattered refugia. The distribution of lineage B, from the South China Sea to the Korean Peninsula, appears to reflect postglacial recolonizations of coastal habitats. These three lineages do not coincide with the three documented morphological formae in C. ocellatus, suggesting that additional cryptic species may exist in this taxon. Our study illustrates the interaction of environmental variability and demographic processes in producing lineage diversification in an intertidal seaweed and highlights the importance of phylogeographic approaches for discovering cryptic marine biodiversity.

opencc-zeroNov 2021View details →

Data from: Pulled diversification rates, lineages-through-time plots and modern macroevolutionary modelling

Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca & Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we illustrate the characteristics of newly-proposed "pulled rates" and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

opencc-by-4.0Jul 2022View details →

Datasets associated with Dale et al. 2022 Diversification and trait evolution in New Zealand woody lineages across changing biomes

Biome occupancy and trait datasets for New Zealand Melicytus, Myrsine, and Pseudopanax species used in Dale et al. 2022 Diversification and trait evolution in New Zealand woody lineages across changing biomes (https://doi.org/10.1080/03036758.2022.2108071). The datasets are biomes occupied, Specific Leaf Area, stem density, leaf nutrient content (N, P, K), and cold sensitivity. "dataset info.txt" outlines the variable names and their units.

opencc-by-4.0Aug 2024View details →

Supplementary Datasets for "Analyses of the effects of selfing on lineage diversification across multiple genera"

The datasets contain the mating system character states, sequence supermatrices and phylogenies used in the study “Analyses of the effects of selfing on lineage diversification across multiple genera”. Please read the "datasets_description.doc" file for a detailed description of the datasets.

opennotspecifiedJul 2024View details →

Figure 2. Phylogenetic structure within Petrodromus. Colour coding indicates the main phylogenetic lineages found. A in Four-toed sengi (Petrodromus tetradactylus, Afrotheria, Mammalia) museomics reveals a crucial role of East African forests in macroscelidean diversification

Figure 2. Phylogenetic structure within Petrodromus. Colour coding indicates the main phylogenetic lineages found. A, Bayesian phylogenetic tree from mitochondrial (less) and nuclear DNA (right) with major genetic lineages highlighted. Numbers indicate posterior probability of deeper nodes. B, Collecting locations of samples assigned to lineages, with squares representing the P.t.s.s. lineages and dots all other lineages. C, Haplotype network of the nuclear gene IRBP (top) and mitochondrial gene 16S rRNA (boưom).

opencc-zeroJul 2021View details →

The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages

While the influence of Pleistocene climatic changes on divergence and speciation has been well-documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. Here, we investigate the role of hydrological and coastal topographic changes brought about by Plio-Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7,958 ddRAD-seq (double digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to investigate the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea-level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter- and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types.

opencc-zeroAug 2021View details →

Data from: Peripheral morphology is associated with restricted lineage diversification and endemism across a large passerine radiation

Aim: Across a variety of taxonomic scales species diversity is unevenly distributed among its constituent units, and clades with few species are more common than expected assuming homogeneous rates of speciation and extinction among lineages. In order to explain the prevalence of species poor families among a global and speciose radiation of passerine birds, we test whether these groups share common eco-morphological, geographic and phylogenetic attributes. Location: Global Time period: Late Oligocene to the present day Major taxa studied: The Corvides (ca. 790 species) Methods: We obtained 10 linear measurements of external morphology for 782 species of corvoid passerines. Using these measurements as a proxy for species ecology, we assessed the positioning of corvoid families in eco-morphological trait space, and how these factors are associated with their species richness and rates of lineage diversification. Subsequently, we compared these same characteristics (species richness, morphological positioning and rates of lineage diversification), between families that are currently endemic to the Australasian ancestral area of the Corvides, with those that have dispersed and diversified throughout other continental and insular landmasses. Results: Families with low species richness and rates of diversification tend to occupy the most peripheral positions in eco-morphological trait space, with almost all of these groups being endemic to Australasia. The peripheral eco-morphological positioning of the Australasian groupings is generally greater than expected upon accounting for differences in phylogenetic isolation and heterogeneity in rates of trait evolution, implying that species poor corvoid families commonly evolved towards marginal areas of morphospace. Main conclusions: The overrepresentation of species poor clades across diverse sets of organismal groups is consistent with their evolution towards, and the maintenance in, marginal areas of ecological niche space. The evolution of peripheral eco-morphological characters represents a potentially significant limit to rates of range expansion and lineage diversification.

opencc-zeroAug 2021View details →

What drives diversification in a pantropical plant lineage with extraordinary capacity for long-distance dispersal and colonisation?

Aim: Colonisation of new areas may entail shifts in diversification rates linked to biogeographic movement (dispersification), which may involve niche evolution if species were not pre-adapted to the new environments. Scleria (Cyperaceae) includes c. 250 species and has a pantropical distribution suggesting an extraordinary capacity for long-distance dispersal and colonisation. We investigate patterns of diversification in Scleria, and whether they are coupled with colonisation events, climate niche shifts or both. Location: Tropics and subtropics. Taxon: Nutrushes Scleria (Cyperaceae). Methods: We used molecular data from three DNA regions sequenced for 278 accessions representing 140 Scleria taxa (53% of species) to develop a chronogram, model ancestral ranges, and measure rates of diversification. Integrating data from 12,978 digitised and georeferenced herbarium records, we investigated niche evolution. Results: High dispersal rates in Scleria, a genus with multiple dispersal syndromes, make reconstruction of ancestral areas at deep nodes in the phylogeny highly equivocal. Main dispersal and colonisation events involve movements from South to Central America (c. 19), from Africa to Madagascar (c. 12), from Asia to Oceania (c. 7), from Africa to South America (c. 7) and Central America to South America (c. 6). Two main shifts in diversification rates happened during the warm period of the Miocene. Main conclusions: Dispersification from South America to Africa without climate niche shift seems to explain the diversification shift in section Hypoporum implying that species were pre-adapted. Shifts in climate niche evolution predate the second shift in diversification rates suggesting lineages were pre-adapted prior to biogeographic movements. Within subgenus Scleria, colonisations of Asia and Madagascar by sections Elatae and Abortivae, respectively, are coupled with niche shifts suggesting that these colonisations involved climate niche adaptation.

Figs. 14–20 in Egg Hatch and First Instar of Semijulistus spectabilis (Lewis) (Coleoptera: Rhadalidae) and Diversification of the Ontogenic Development of the Melyrid Lineage

Figs. 14–20. Adult sternites: 14) Semijulitus spectabilis (Rhadalidae); 15) Cordylepherus xantholoma (Kiesenwetter) (Melyridae, Malachiinae); 16) Dasytes vulgaris (Melyridae, Dasytinae). Eggs at oviposition: 17) Holzschuhus yoronensis (from Asano 2019); 18) Laius asahinai; 19) Attalus elongatulus (from Asano 2018); 20) D. vulgaris (from Asano 2016).

Figs. 1–4 in Egg Hatch and First Instar of Semijulistus spectabilis (Lewis) (Coleoptera: Rhadalidae) and Diversification of the Ontogenic Development of the Melyrid Lineage

Figs. 1–4. First instar and egg of Semijulitus spectabilis. 1) Dorsal habitus; 2–3) Head, dorsal and ventral views, respectively; 4) Egg. Scale bar A: Fig 1; scale bar B: Figs. 2–3; scale bar C: Fig. 4.

Figs. 21–28 in Egg Hatch and First Instar of Semijulistus spectabilis (Lewis) (Coleoptera: Rhadalidae) and Diversification of the Ontogenic Development of the Melyrid Lineage

Figs. 21–28. Early instars of melyrid beetles. 21) Laius asahinai, first instar; 22) Laius asahinai, second instar; 23) Intybia niponicus, first instar; 24) Nepachys japonicus, first instar; 25) Holzschuhus yoronensis, first instar; 26) Attalus elongatulus, first instar; 27) Dasytes vulgaris, embryo after egg burst, msb = egg burster of mesonotum; mtb, = egg burster of metanotum, prb = egg pronotum; 28) D. vulgaris, first instar. Scale bars = 0.2 mm. Figs. 21 and 22 from Asano and Kojima (2013); Fig. 23 from Asano (2013); Fig. 24 from Asano (2014); Fig. 25 from Asano (2018); Fig. 26 from Asano (2017); Figs. 27 and 28 from Asano (2016).

Figs. 5–13. Semijulitus spectabilis. 5 in Egg Hatch and First Instar of Semijulistus spectabilis (Lewis) (Coleoptera: Rhadalidae) and Diversification of the Ontogenic Development of the Melyrid Lineage

Figs. 5–13. Semijulitus spectabilis. 5) Habitat; 6) Mating; 7) Feeding; 8) Eggs at oviposition; 9) Eggs at egg burst; 10) Chorion after hatching; 11) First instar hiding in bark crevice; 12) Egg hatch; 13) First instar, ventral view. 1L = first instar; cr = chorion; y = yolk.

Figs. 29–34 in Egg Hatch and First Instar of Semijulistus spectabilis (Lewis) (Coleoptera: Rhadalidae) and Diversification of the Ontogenic Development of the Melyrid Lineage

Figs. 29–34. Egg bursters of Melyridae. 29) Laius asahinai (from Asano and Kojima (2013); 30) Attalus elongatulus (from Asano 2018); 31) Nepachys japoni; 32) Malachius prolongatus (from Asano 2017); 33) Holzschuhus yoronensis (from Asano 2019); 34) Dasytes vulgaris (from Asano 2016).

opencc-zeroSep 2021View details →

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

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

Figure 10 in The evolution of an ancient tapeworm lineage in its catfish hosts: vicariance, dispersal and diversification in Gangesiinae (Cestoda: Proteocephalidae)

Figure 10. Palaeogeographic map of the Early Miocene, 20 Mya (C. Scotese, Palaeoatlas, v.3). Siluridae have originated. Dashed arrows show the major dispersal routes of Gangesiinae. Range expansion of Siluridae into northern Africa allowed host-shifting into Malapteruridae. Dispersal and diversification of Gangesiinae, especially Gangesia, continued in the Indomalayan region and extended to north-east Asia. The rectangular box with an 'x' mark inside it indicates the absence of gangesiine tapeworms in catfish hosts. Sigmoid marks indicate the presence of Gangesiinae in catfish hosts.

Figure 8 in The evolution of an ancient tapeworm lineage in its catfish hosts: vicariance, dispersal and diversification in Gangesiinae (Cestoda: Proteocephalidae)

Figure 8. Palaeogeographic map of the Late Aptian, 115 Mya (C. Scotese, Palaeoatlas, v.3), showing the origin of the Siluriformes (catfishes) in South America with subsequent dispersal to Africa or an origin in Gondwana when Africa and South America were still united, followed by vicariance. The presence of siluriforms in India during this time is questionable. Siluriforms are absent from Eurasia at this time (see text for discussion). The '?' mark on the catfish in Africa indicates the uncertainty about the Gangesiinae in catfishes on that landmass at the time. The '?' mark on the Indian landmass (IND) indicates that it is uncertain if catfishes were present on that landmass at the time. Abbreviations: AUS, Australian region; INM, Indomalayan region; PAL, Palaearctic region.

Figure 9 in The evolution of an ancient tapeworm lineage in its catfish hosts: vicariance, dispersal and diversification in Gangesiinae (Cestoda: Proteocephalidae)

Figure 9. Palaeogeographic map of the Middle Eocene, 40 Mya (C. Scotese, Palaeoatlas, v.3). Siluroid hosts of some major lineages of Gangesiinae are already present: Malapterurus in Africa, and Rita and Pangasius in Asia. Families of other siluroid hosts of Gangesiinae, such as Schilbeidae and Bagridae, have also originated by this time. Silurus is yet to appear. Gangesiinae have originated in the Indomalayan region by this time but are absent in Europe and Africa. Their presence in siluroids outside the Indomalayan region during this time is uncertain. Rectangular boxes with 'x' marks inside them indicate the absence of gangesiine tapeworms in catfish hosts. The '?' mark on catfishes indicates that the presence of Gangesiinae in these hosts is uncertain. Sigmoid marks indicate the presence of Gangesiinae in catfish hosts.

Figure 7 in The evolution of an ancient tapeworm lineage in its catfish hosts: vicariance, dispersal and diversification in Gangesiinae (Cestoda: Proteocephalidae)

Figure 7. Present-day distribution of major lineages (genera) of Gangesiinae, showing varying levels of disjunct distribution in Electrotaenia, Gangesia, Postgangesia and Silurotaenia, and the endemic nature of other genera such as Pangasiocestus, Ritacestus and Vermaia.

Figure 6 in The evolution of an ancient tapeworm lineage in its catfish hosts: vicariance, dispersal and diversification in Gangesiinae (Cestoda: Proteocephalidae)

Figure 6. Scanning electron micrographs of Gangesia mukutmanipurensis sp. nov. from Ompok bimaculatus. A, scolex, subapical view. B, scolex, dorsoventral view. C, detail of rostellum-like organ. D, sucker with coniform spinitriches on the outer rim. E, F, detail of outer rim of the sucker with coniform spinitriches. G, detail of capilliform filitriches on the rostellumlike organ. H, detail of coniform spinitriches on the rostellum-like organ. I, detail of gladiate spinitriches on the neck region.

Figure 5 in The evolution of an ancient tapeworm lineage in its catfish hosts: vicariance, dispersal and diversification in Gangesiinae (Cestoda: Proteocephalidae)

Figure 5. Line drawings of Gangesia mukutmanipurensis sp. nov. from Ompok bimaculatus (specimen accession number in parentheses). A, scolex, subapical view (ZSI/W11086/1). B, C, scolex, dorsoventral view (ZSI/W11085/1 and ZSI/W11082/1/1). D, frontal section of the scolex (ZSI/W11087/1). E, mature proglottid, ventral view (ZSI/W11084/1). F, terminal genitalia (ZSI/W11083/1/2). G, egg drawn in distilled water. Abbreviations: cc, chromophil cell; cs, cirrus-sac; doc, dorsal osmoregulatory canal; eh, embryonic hook; em, embryophore; ga, genital atrium; mi, microtriches; oc, osmoregulatory canal; oe, outer envelope; on, oncosphere; ov, ovary; re, retractor muscles; ro, rostellum-like organ; su, sucker; te, testes; up, uterine pore; va, vagina; vf, vitelline follicles; voc, ventral osmoregulatory canal; vs, vaginal sphincter.