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opennotspecifiedJul 2024View details →

Figure 1 in Removal of historical taxonomic bias and its impact on biogeographic analyses: a case study of Neotropical tardigrade fauna

Figure 1. Biogeographic compartmentalisation of provinces from the Andean and Neotropical regions proposed by Morrone (2015) and Morrone et al. (2022), respectively. The hierarchy of compartmentalisation is from highest to lowest level: region, transition zone, subregion, dominion, and province. Each level can be subdivided into multiple lower levels under their name (e.g., a region consisting of several subregions). Each biogeographic province is coloured according to its transition zone, subregion or dominion. The Neotropical region (NR), in this study, is composed of the Antillean subregion (ASR), Brazilian subregion (BSR) and Chacoan subregion (CSR). The BSR is composed of the Mesoamerican dominion (MD), Pacific dominion (PD), Boreal Brazilian dominion (BBD) and South Brazilian dominion (BBD). The CSR is composed of the Southeastern Amazonian dominion (SAD), Chacoan dominion (CD) and Paraná dominion (PD). The Andean region (AR), in this study, is composed of the Central Chilean subregion (CCSR), Subantarctic subregion (SSR) and Patagonian subregion (PSR). The acronym for each region, transition zone, subregion or dominion is presented next to its name. Under each subregion or dominion, the names of the comprising provinces are listed. The nature of the records present in each province is indicated by an icon of a coloured tardigrade next to its name: provinces without records of tardigrade species (red tardigrade), provinces with only records of 'false cosmopolitan species' (blue tardigrade), provinces with records of 'false cosmopolitan' and 'indigenous species' (orange tardigrade), and provinces with only records of 'indigenous species' (violet tardigrade). The tardigrade icon is in the public domain and was obtained from Phylopic (https://www.phylopic.org).

opennotspecifiedJul 2024View details →

Figure 5 in Removal of historical taxonomic bias and its impact on biogeographic analyses: a case study of Neotropical tardigrade fauna

Figure 5. Tanglegram of consensus tree exhibiting the similarity between all biogeographic provinces from biogeographic regions and transitions zones (Andean region (AR), South American transition zone (SATZ), Neotropical region (NR), and Mexican transition zone (MTZ)) for all data ('false cosmopolitan' and 'indigenous species', on the left) and only 'indigenous data' (on the right). Each province is connected to itself by a dark grey line. The consensus tree was obtained by resampling (1000×) the row order with the 'recluster' package (Dapporto et al. 2020). Each province is coloured according to their area of origin: provinces from the AR are coloured blue, provinces from the SATZ are coloured light green, provinces from the NR are coloured pink, and provinces from the MTZ are coloured purple. Branches of provinces that appear unrelated to any other are bold and red-coloured. Provinces without any records of 'indigenous species' are not present in the tanglegram. Provinces without any records of tardigrade species were excluded from the clustering analysis.

opennotspecifiedJul 2024View details →

Table 2 in Removal of historical taxonomic bias and its impact on biogeographic analyses: a case study of Neotropical tardigrade fauna

Table 2. Extrapolated richness of limnoterrestrial and freshwater tardigrade species and standard error for each region and transition zone. Estimations were made with all data (‘false cosmopolitan’ and ‘indigenous species’) and only ‘indigenous data for comparison. Estimations were made using the Jackknife1 estimator (based on: Burnham and Overton 1978, 1979).<table><tbody><tr><th>Area</th><th>Dataset</th><th>Number of provinces with at least one record</th><th>Total number of provinces</th><th>Observed richness</th><th>Estimated richness</th><th>Standard error</th></tr></tbody><tbody><tr><th>Neotropical region</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>33</td><td>50</td><td>186</td><td>282.969</td><td>29.094</td></tr><tr><td>‘Indigenous data’</td><td>29</td><td>50</td><td>96</td><td>157.793</td><td>19.499</td></tr><tr><th>Andean region</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>7</td><td>9</td><td>105</td><td>159.857</td><td>31.489</td></tr><tr><td>‘Indigenous data’</td><td>7</td><td>9</td><td>43</td><td>68.714</td><td>14.154</td></tr><tr><th>South America transition zone</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>6</td><td>7</td><td>66</td><td>102.666</td><td>25.011</td></tr><tr><td>‘Indigenous data’</td><td>3</td><td>7</td><td>26</td><td>41.330</td><td>12.995</td></tr><tr><th>Mexican transition zone</th><td>All data (‘false cosmopolitan’ and ‘indigenous species’)</td><td>5</td><td>5</td><td>41</td><td>65.800</td><td>14.881</td></tr><tr><td>‘Indigenous data’</td><td>4</td><td>5</td><td>11</td><td>19.250</td><td>5.068</td></tr></tbody></table>

opencc-by-4.0Sep 2024View details →

SAFRAN Present Forcing (Historical: 2004/2014) and Future projections (RCP4.5 and RCP8.5: 2041/2060).

SAFRAN forcing refers to a set of meteorological data used to model the climate, covering both historical periods (2004-2014) and future projections under two greenhouse gas concentration scenarios (RCP4.5 and RCP8.5) for the period 2041-2060. Each dataset includes key parameters for climate analysis: cloud cover (NB), humidity (QA), direct radiation (RD), infrared radiation (RI), precipitation (RR), visible radiation (RV), snow cover (SS), temperature (TA), and wind strength (UA). These parameters are measured on a grid with variable resolution, ranging from 8 km in plains to 1 km in mountains and irrigated agricultural lands. This data is essential for understanding current and future atmospheric dynamics in the context of climate change.

opennotspecifiedMay 2023View details →

Figures 1–18 in Staurosirella eruciformis, a new Staurosirella (Bacillariophyta) species from a historic sample from Scotland, UK

Figures 1–18. Staurosirella eruciformis Van de Vijver sp. nov. LM and SEM images taken from the holotype sample (BR-4785, Hawthorden, Scotland, UK, Walker Arnott sample WA245). 1–14. LM views of the population arranged in decreasing length. 15–17. Three SEM external views of an entire valve. Note the presence of the irregular groups of marginal spines and the rather well-developed apical pore field at each apex. The virgae and sternum are clearly raised with the striae as punch-holes. 18. SEM internal view of an entire valve. Scale bars = 10 µm.

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r14)

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r14)

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r2)

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r2)

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r6)

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r6)

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r3)

APECOSM outputs used in the Earth's Future "Past and Future of Marine Ecosystems" special issue (historical-r3)

Data from: Speciation and historical invasions of the Asian black-spined toad (Duttaphrynus melanostictus)

This data package includes the following datasets analyzed in the corresponding publication:  <ul> <li>An alignment (fasta format) of 130,792 bp concatenating the RAD tags present in at least 80 of the 88 Duttaphrynus samples considered (Duttaphrynus_ddRADseq_n88p80_131kb.fas). It was used to produce the tree presented in Supplementary Fig. 1.</li> <li>An alignment (fasta format) of 83,652 bp concatenating the RAD tags present in 25 unadmixed Duttaphrynus samples (Duttaphrynus_ddRADseq_n25p25_84kb.fas). It was used in the phylogenetic analyses presented in Fig. 1a and Supplementary Fig. 2.</li> <li>Two alignments (fasta format) of 482,648 bp and 628,293 bp concatenating the RAD tags present in 17 and 52 samples of D. melanostictus s. s. and D. cf. melanostictus, respectively (Duttaphrynus_melanostictus_ss_West_n17p17_483kb.fas and Duttaphrynus_cf_melanostictus_East_n52p52_628kb.fas). These were used in the network analyses presented in Fig. 2b.</li> <li>Three matrices of 851 SNPs, 3364 SNPs and 4782 SNPs, genotyped in 69, 17 and 52 samples of D. melanostictus s. l., D. melanostictus s. s. and D. cf. melanostictus, respectively (Duttaphrynus_melanostictus_sl_n69p69wrs_851SNPs.str, Duttaphrynus_melanostictus_ss_West_n17p17wrs_3364SNPs.str, Duttaphrynus_cf_melanostictus_East_n52p52wrs_4782SNPs.str). These were used in the Bayesian clustering and PCA analyses presented in Fig. 2a and Supplementary Figs. 3-4.</li> <li>An alignement (fasta format) of 383 sequences of the mitochondrial gene 16S (558 bp), including 382 sequences of Duttaphrynus + 1 outgroup (Duttaphrynus_16S.fas). It was used in the network analysis presented in Fig. 3b and the phylogenetic analysis presented in Supplementary Fig. 5.</li> <li>An alignement (fasta format) of 495 sequences of the mitochondrial gene ND3 (469 bp), including 494 sequences of Duttaphrynus + 1 outgroup (Duttaphrynus_ND3.fas). It was used in the network analysis presented in Fig. 3b and the phylogenetic analysis presented in Supplementary Fig. 6.</li> <li>An alignement (fasta format) of 27 full or partial mitogenomes (16,844 bp), including 26 sequences of Duttaphrynus + 1 outgroup (Duttaphrynus_mitogenomes.fas). It was used in the phylogenetic analyses presented in Fig. 1b and Supplementary Fig. 7.</li> </ul> The meta-data associated to these datasets are provided in the corresponding publication (Supplementary Data 1 and 4).

Data from: Spatiotemporal diversification of the true frogs (Genus Rana): a historical framework for a widely studied group of model organisms

True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci sampled from most species of Rana, and use that phylogeny to clarify the group's diversification and global biogeography. Our analyses consistently support an "Out of Asia" pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of diversification; diversification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29–18 Ma. Net diversification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci.

opencc-zeroDec 2014View details →

Data from: Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia

Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.

Data from: Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.

opencc-zeroDec 2011View details →

Data from: Persistent genetic signatures of historic climatic events in an Antarctic octopus

Repeated cycles of glaciation have had major impacts on the distribution of genetic diversity of the Antarctic marine fauna. During glacial periods, ice cover limited the amount of benthic habitat on the continental shelf. Conversely, more habitat and possibly altered seaways, were available during interglacials when the ice receded and the sea level was higher. We used microsatellites and partial sequences of the mitochondrial cytochrome oxidase c subunit 1 (MT-CO1) gene to examine genetic structure in the direct-developing, endemic Southern Ocean octopod Pareledone turqueti Joubin, 1905 sampled from a broad range of areas that circumvent the Antarctic continent. We find that, unusually for a species with poor dispersal potential, P. turqueti has a circumpolar distribution and is also found off the islands of South Georgia and Shag Rocks. The overriding pattern of spatial genetic structure can be explained by hydrographic (with ocean currents both facilitating and hindering gene flow) and bathymetric features. The Antarctic Peninsula region displays a complex population structure, consistent with its varied topographic and oceanographic influences. Genetic similarities between the Ross and Weddell Seas, however, are interpreted as a persistent historic genetic signature of connectivity during the hypothesized Pleistocene Western Antarctic Ice Sheet collapses. A calibrated molecular clock indicates two major lineages within P. turqueti, a continental lineage and a subAntarctic lineage, that diverged in the mid-Pliocene with no subsequent gene flow. Both lineages survived subsequent major glacial cycles. Our data are indicative of potential refugia around the Antarctic continent within the Ross Sea, Weddell Sea and off Adélie Land, with mean age of mtDNA diversity within these main continental lineages coinciding with Pleistocene glacial cycles.

Data from: The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird

Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variation among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using eleven microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST) and phenotypic differentiation (PST) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact mid-way up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients.

opencc-zeroJul 2019View details →

Data from: Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex

Background: Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex. Results: We generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade. Conclusions: We found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, "stepping-stone" dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea.

opencc-zeroDec 2013View details →

Data from: Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna

Recent molecular hypotheses suggest that some traditional suprageneric taxa of Characiformes require revision, as they may not constitute monophyletic groups. This is the case for the Bryconidae. Various studies have proposed that this family (considered a subfamily by some authors) may be composed of different genera. However, until now, no phylogenetic study of all putative genera has been conducted. In the present study, we analyzed 27 species (46 specimens) of all currently recognized genera of the Bryconidae (ingroup) and 208 species representing all other families and most genera of the Characiformes (outgroup). Five genes were sequenced: 16SrRNA, Cytochrome b, recombination activating gene 1 and 2 and myosin heavy chain 6 cardiac muscle. The final matrix contained 4699 bp and was analyzed by maximum likelihood, maximum parsimony and Bayesian analyses. The results show that the Bryconidae, composed of Brycon, Chilobrycon, Henochilus and Salminus, is monophyletic and is the sister group of Gasteropelecidae + Triportheidae. However, the genus Brycon is polyphyletic. Fossil studies suggest that the family originated approximately 33 million years ago (Ma) and that one of the two main lineages persisted only in trans-Andean rivers, including Central American rivers, suggesting a much older origin of Mesoamerican ichthyofauna than previously accepted. Bryconidae is composed by five main clades, including the genera Brycon, Chilobrycon, Henochilus and Salminus, but a taxonomic review of these groups is needed. Our results points to a possible ancient invasion of Central America, dating about 17.4+/-8 Ma (late Oligocene/late Miocene), to explain the occurrence of Brycon in Central America.

Data from: Phylogenetics, delimitation and historical biogeography of the pantropical tree genus Thespesia (Malvaceae, Gossypieae)

Thespesia consists of 16 species of trees and shrubs from Southeast Asia–Oceania, Africa and America, the most well known being T. populnea, a small tree of tropical coastal areas around the world. Phylogenetic relationships in the genus and among its allies in tribe Gossypieae were inferred using three plastid and two nuclear regions to ascertain its generic delimitation and explore its biogeographical history. Maximum-likelihood and Bayesian analyses confirmed that Thespesia is not monophyletic and, based on these results, Azanza is reinstated to accommodate the two species previously placed in Thespesia section Lampas. Dating analyses and ancestral range estimation indicated that Thespesia s.s. most likely originated in Southeast Asia–Oceania c. 30 Mya, but extant species did not begin to differentiate until the late Miocene. Two dispersal events, one into Africa c. 11 Mya and another into America (Antilles) c. 9 Mya, gave rise to the African and the Greater Antillean endemics, respectively. The two most widespread hydrochorous species, T. populnea and T. populneoides, originated in Southeast Asia–Oceania from where they spread to other parts of the world. Our analysis also indicated a much earlier origin than previously reported for Eumalvoideae and its tribes, suggesting that vicariance might have had an important role early in the history of these groups.

opencc-zeroDec 2011View details →

Data from: The interplay of dispersal limitation, rivers, and historical events shapes the genetic structure of an Amazonian frog

Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined Cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a ~6 km transect to evaluate dispersal ability and between paired bank populations along a ~65 km stretch of the Approuague river to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale and conclude that the species has a restricted dispersal ability likely tied to its life history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is due to restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life history traits comparable to Adenomera andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity.