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opennotspecifiedMay 2010View details →

Figure 2 in Global historical biogeography of hadrosaurid dinosaurs

Figure 2. Time-calibrated phylogram of Hadrosauroidea based on the reduced strict consensus tree of Prieto-Márquez (2010). Letters at each node represent ancestral areas as inferred in the dispersal–vicariance analysis; their meaning is as in Fig. 1. The colours of the stratigraphical ranges of taxa indicate the following areas: white, Europe; black, North America; light grey, Asia; dark grey, range of an entire clade. Black stars indicate vicariance. Arrows indicate the direction of dispersal events. Note that the stratigraphical ranges for each species are not point estimates, but just extend to indicate divisions of particular geochronological stages. Geochronological ages from Gradstein, Ogg, Smith (2004). Abbreviations: a, North America; b, South America; c, Europe; d, Asia; ab, North and South America; ac, North America and Europe; ad, North America and Asia; cd, Eurasia.

opennotspecifiedMay 2010View details →

Figure 1 in Global historical biogeography of hadrosaurid dinosaurs

Figure 1. Reduced strict consensus tree derived from parsimony analysis of hadrosauroid dinosaurs by Prieto-Márquez (2010), showing ancestral area reconstructions for all the nodes. Words between quotation marks are informal names created to facilitate the reference to specific clades throughout the text. Abbreviations: a, North America; b, South America; c, Europe; d, Asia; ab, North and South America; ac, North America and Europe; ad, North America and Asia; cd, Eurasia.

opennotspecifiedMay 2010View details →

Figure 7 in Global historical biogeography of hadrosaurid dinosaurs

Figure 7. Distribution of the main hadrosaurid clades discussed in the text on a paleogeographic reconstruction of continental coastlines during the Maastrichtian. Continental paleocoastlines redrawn after Smith et al. (1994), Hay et al. (1999), Blakey (2001), Pough et al. (2004), and Hedges (2006).

opencc-zeroJan 2022View details →

A timeframe for mint evolution: Towards a better understanding of trait evolution and historical biogeography in Lamiaceae

The mint family (Lamiaceae) is one of the largest and most economically important families of flowering plants. Despite focused study on relationships within subclades, higher-level relationships have been understudied. Moreover, the herbaceous habit of much of the family has resulted in a poor fossil record and has hampered estimates of divergence times. Using a new dataset of five plastid loci from 178 Lamiaceae representing all subfamilies and nearly all tribes, we clarify major infrafamilial relationships and present a robust set of divergence times. We use this phylogenetic hypothesis as a platform to test prior hypotheses regarding the historical biogeography and evolution of major traits within the family. We confirm the placement of subfamily Nepetoideae, show continued uncertainty in the placement of subfamilies Ajugoideae and Premnoideae, and highlight extreme discordance with recent results from nuclear data. Lamiaceae originated during the Late Cretaceous as a woody plant with a nutlet fruit and four stamens, probably in Southeast Asia. Most subfamilies diverged during the Eocene, perhaps facilitated by climatic cooling. Our results provide a valuable set of secondary dates for Lamiaceae and highlight the need for focused study of subfamilies Callicarpoideae and Viticoideae. Our results also provide several hypotheses regarding trait or range-dependent diversification.

opencc-zeroFeb 2022View details →

Historical biogeography and character-mapping of Hiptage (Malpighiaceae) corroborate Indochina's rainforests as one of the main sources of plant diversity in Southeastern Asia

In Malpighiaceae, Hiptage represents one of the seven past dispersal events from the Neotropics to the Paleotropical region, being by far the most widely diversified and distributed genus of Paleotropical Malpighiaceae. In this study, we tested the monophyly of the current infrageneric classification of Hiptage with a dated and calibrated molecular phylogeny. We also reconstructed ancestral areas to elucidate which route led to the colonization of Southeast Asia by the most recent common ancestor (MRCA) of this genus (Mainland or Indian routes). The pre-existing infrageneric classification of Hiptage was recovered as non-monophyletic due to being solely based on homoplasic morphological characters, such as the presence and number of sepal nectar glands. Regarding its biogeography, the MRCA of Hiptage arose in the rainforests of southeast Asia ca. 24.0 Mya and greatly diversified in this region. Few lineages have dispersed eastward to the pacific islands or westwards to India. Based on our results, we hypothesize that the MRCA of Hiptage did not take the Indian route to reach Southeastern Asia. Instead, it reached this region by past mainland forest connections between North America-Europe (Boreotropical hypothesis) and southeast Asia. Nonetheless, distribution ranges for the species of Hiptage must be carefully revised, and the five species of Hiptage endemic to India must also be sampled so we can properly test which route led the MRCA of Hiptage to reach Southeast Asia in the early Miocene.

opencc-zeroFeb 2022View details →

Data from: A diversification relay race from Caribbean-Mesoamerica to the Andes: historical biogeography of Xylophanes hawkmoths

The regions of the Andes and Caribbean-Mesoamerica are both hypothesized to be the cradle for many Neotropical lineages, but few studies have fully investigated the dynamics and interactions between Neotropical bioregions. The NewWorld hawkmoth genus Xylophanes is the most taxonomically diverse genus in the Sphingidae, with the highest endemism and richness in the Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA barcode data and generated the first time-calibrated tree for this genus, covering 93.8% of the species diversity. We used event-based likelihood ancestral area estimation and biogeographic stochastic mapping to examine the speciation and dispersal dynamics of Xylophanes across bioregions. We also used trait-dependent diversification models to compare speciation and extinction rates of lineages associated with different bioregions. Our results indicate that Xylophanes originated in Caribbean-Mesoamerica in the Late Miocene, and immediately diverged into five major clades. The current species diversity and distribution of Xylophanes can be explained by two consecutive phases. In the first phase, the highest Xylophanes speciation and emigration rates occurred in the Caribbean-Mesoamerica, and the highest immigration rates occurred in the Andes, whereas in the second phase the highest immigration rates were found in Amazonia, and the Andes had the highest speciation and emigration rates.

opencc-zeroMar 2022View details →

Connecting Amazonian historical biogeography and local assemblages of understorey birds: recurrent guild proportionality within areas of endemism.

Aim: Current diversity patterns in local communities result from historical and contemporary events that operate at distinct spatial and temporal scales. However, the contribution of local and large-scale processes in structuring species diversity remain a contentious topic in ecology. We investigated diversity patterns (species richness, composition and number of captures) of understorey bird assemblages in Amazonian unflooded (terra firme) forests. We sought to understand whether understorey bird assemblages in distinct areas of endemism show distinct patterns of diversity, and whether species replacements among areas of endemism occur while the proportion of species within guilds remains stable. Location: Amazonia. Taxon: Understorey birds. Methods: To investigate diversity patterns, we compiled studies that mist-netted birds at 11 regions across seven Amazonian areas of endemism. We used coverage-based rarefaction curves, non-metric multidimensional scaling (NMDS) and created a heatmap based on the proportion of captures in each area of endemism to access patterns of richness, composition and captures of understorey birds, respectively. The relative variance (RVgp index) was calculated to investigate the existence of guild proportionality within each area of endemism. Results: Bird assemblages diverged across the seven areas of endemism, in terms of species richness, composition and captures. However, the proportion of species and individuals within guilds was similar among areas of endemism, indicating that species replacements across areas of endemism occur while maintaining the same ecological functions. Guild proportionality suggests that interspecific competition and resource availability are more important than environmental heterogeneity in structuring understorey bird assemblages. Main conclusions: The similar proportion of species within guilds suggest that interspecific competition and resource availability are more important than environmental heterogeneity in structuring local assemblages, possibly via a process of limiting similarity in morphological and functional traits. The observed congruent structure in understorey bird assemblages across areas of endemism shows that coupled historical and ecological processes, operating at local to large scales, have led to current patterns of diversity and composition in Amazonian bird communities.

opencc-zeroApr 2022View details →

Data from: Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura)

The genus Cyclura includes nine extant species and six subspecies of West Indian Rock Iguanas and is one of the most imperiled genera of squamate reptiles globally. An understanding of species diversity, evolutionary relationships, diversification, and historical biogeography in this group is crucial for implementing sound long-term conservation strategies. We collected DNA samples from 1–10 individuals per taxon from all Cyclura taxa (n = 70 ingroup individuals), focusing where possible on incorporating individuals from different populations of each species. We also collected 1–2 individuals from each of seven outgroup species of iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei (n = 12 outgroup individuals). We used targeted genomic sequence capture to isolate and to sequence 1,872 loci comprising of 687,308 base pairs (bp) from each of the 82 individuals from across the nuclear genome. We extracted mitochondrial reads and assembled and annotated mitogenomes for all Cyclura taxa plus outgroup species. We present well-supported phylogenomic gene tree/species tree analyses for all extant species of Cyclura using ASTRAL-III, SVDQuartets, and starBEAST methods, and discuss the taxonomic, biogeographic, and conservation implications of these data. We find a most recent common ancestor of the genus 9.91 million years ago. The earliest divergence within Cyclura separates C. pinguis from a clade comprising all Cyclura except C. pinguis. Within the latter group, a clade comprising C. carinata from the southern Lucayan Islands and C. ricordii from Hispaniola is the sister taxon to a clade comprising the other Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri (from Hispaniola and Isla Mona) form the sister taxon to a clade of species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila), and the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura cychlura and C. rileyi form a clade whose sister taxon is C. nubila. Cyclura collei is the sister taxon to these three species combined.

opencc-zeroAug 2022View details →

Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles

Cerambycinae is the second-largest subfamily of longhorn beetles in the Southern Hemisphere. The phylogeny of Cerambycinae is poorly known, resulting in a highly artificial tribal-level classification and a largely speculative evolutionary history. We reconstructed the phylogenetic relationships of Cerambycinae at the generic level using anchored hybrid enrichment data from hundreds of nuclear genes, with a primary focus on the extraordinarily diverse faunas of Australia and New Zealand. We also estimated divergence times by incorporating fossil calibrations in our analyses. We identified two main clades within Cerambycinae, which can also be separated morphologically by a distinct type of antennal foramen. We recovered a Late Jurassic origin of crown Cerambycinae. Dorcasominae, which was newly found to have representatives in Australia, was notably derived from within Cerambycinae. We recovered two independent origins of Australian Cerambycinae: one clade originated in the Early Cretaceous and is likely endemic to the Southern Hemisphere, while the other clade appears to have immigrated to Australia, perhaps from the Northern Hemisphere. Within the Australian lineages were multiple independent origins of New Zealand taxa, all of which are relative host-plant generalists. Tribal relationships and assignments are discussed and, based on our results, the following major nomenclatural acts were made: Dorcasominae Lacordaire, 1868, is downgraded to a tribe Dorcasomini of Cerambycinae Latreille, 1804; Neostenini Lacordaire, 1868 syn. nov. is treated as a junior synonym of Uracanthini Blanchard, 1851.

opennotspecifiedOct 2019View details →

Fig. 2 in Historical Biogeography of Holarctic Cymbiodyta Water Scavenger Beetles in the Times of Cenozoic Land Bridge Dispersal Routes

Fig. 2. Bayesian median divergence time estimates of Cymbiodyta. Maximum clade credibility chronogram resulting from the best BEAST analysis using secondary calibrations with outgroups pruned.The credibility intervals are indicated with gray horizontal boxes.The best ancestral range estimation scheme from the DEC analyses is presented with the most likely ancestral range for each node along the phylogeny of the genus. Color codes follow the inserted caption.

opennotspecifiedOct 2019View details →

Fig. 1 in Historical Biogeography of Holarctic Cymbiodyta Water Scavenger Beetles in the Times of Cenozoic Land Bridge Dispersal Routes

Fig. 1. Molecular phylogeny of the genus Cymbiodyta and phylogenetically closely related genera. MrBayes topology inferred based on the concatenated data set of five gene fragments. Nodal support for each node resulting from the MrBayes and IQ-TREE analyses is given following the inserted caption. A picture of Cymbiodyta marginella (Fabricius, 1792) is presented (Credit: Udo Shmidt).

opencc-by-4.0Oct 2019View details →

Historical biogeography of the widespread macroalga Sargassum (Fucales, Phaeophyceae)

Datasets and supplementary material

opennotspecifiedJan 2017View details →

Fig. 1 Mitochondrial genome structure and genes variability. a in Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae)

Fig. 1 Mitochondrial genome structure and genes variability. a Mitogenomes of Paramuricea clavata and Paramuricea macrospina with genome size and gene annotation. GC-content and AT-content are shown in blue and green on the inner and outer surface of the ring, respectively. b Sliding window analysis of the complete mitochondrial genomes of P. clavata and P. macrospina. The black line indicates

opennotspecifiedJul 2012View details →

Fig. 1 in Historical biogeography of tits (Aves: Paridae, Remizidae)

Fig. 1 Breeding distribution of extant parid and remizid tit species according to BirdLife International and NatureServe (2011) subdivided into ten areas (A–J) with number of Paroidea species per area and connectivity among areas (Table 1)

opennotspecifiedJul 2012View details →

Fig. 2 in Historical biogeography of tits (Aves: Paridae, Remizidae)

Fig. 2 Molecular phylogeny of Paroidea (tits and penduline tits) based on up to 2035 bp in a 4404-bp alignment of up to four genes (for details see Table S1) reconstructed in BEAST (genes and codon positions partitioned, GTR/HKY models, 100,000,000 generations). At the tips are all extant species recognized in this study for which any sequence was available on GenBank, preceded by distributional areas (see Table 1) in parentheses; at the nodes are posterior probabilities and ancestral-area reconstructions from S-DIVA (maxarea 0 7) as pie charts (color does not refer to a certain area, but to percentage of area combinations in decreasing order)

Fig. 3 Most probable tree resulting from a in Phylogenetics and historical biogeography of Encyclia (Laeliinae: Orchidaceae) with an emphasis on the E. adenocarpos complex, a new species, and a preliminary species list for the genus

Fig. 3 Most probable tree resulting from a Bayesian Inference Analysis of Encyclia using a supermatrix of the regions ITS + rpl32-trnL, trnL-F, ycf1. Black dots above the lines represent Posterior Probabilities> 95%. Stars below the lines are bootstrap support> 70%.

Fig. 2 Strict consensus resulting from a in Phylogenetics and historical biogeography of Encyclia (Laeliinae: Orchidaceae) with an emphasis on the E. adenocarpos complex, a new species, and a preliminary species list for the genus

Fig. 2 Strict consensus resulting from a Maximum Parsimony Analysis of Encyclia using a supermatrix of the regions ITS + rpl32-trnL, trnL-F, ycf1. Stars above the nodes are bootstrap support> 70%. The large star indicates the basal node of Encyclia

Fig. 12 in Phylogenetics and historical biogeography of Encyclia (Laeliinae: Orchidaceae) with an emphasis on the E. adenocarpos complex, a new species, and a preliminary species list for the genus

Fig. 12 Distribution of species of the Encyclia adenocarpos complex. Above: distribution along the western coast of Megamexico. Below: detail of the distributional area of E. mariaeugeniae (maps by WCI)

Fig. 1 in Phylogenetics and historical biogeography of Encyclia (Laeliinae: Orchidaceae) with an emphasis on the E. adenocarpos complex, a new species, and a preliminary species list for the genus

Fig. 1 Major biogeographical areas for the distribution of Encyclia. See section of Materials and Methods for details