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FIGURE 1 in The advertisement call of Physalaemus caete Pombal & Madureira, 1997 (Anura Leptodactylidae: Leiuperinae), an endangered species endemic to Brazil's northern Atlantic Forest
FIGURE 1. (A–C) Spectrogram, oscillogram, and amplitude spectrum, respectively, of the advertisement call of Physalaemus caete from Igarassu (state of Pernambuco, northeastern Brazil). The dominant harmonic (H4) and adjacent harmonics (H3 and H5) are indicated. The fundamental and second harmonics are supposedly filtered out (see text). (D) Male voucher of P. caete (CHPUFRPE 5840; SVL = 23.0 mm).
Data from: Consistent condom use among highly effective contraceptive users in an HIV-endemic area in rural Kenya
<p><strong>Background</strong>: Women of reproductive age are at the highest risk of both HIV infection and unintended pregnancy in sub-Saharan Africa. Highly effective contraceptives (HECs) such as hormonal injectable and implants are widely used in this region. HECs are effective for preventing pregnancies. However, unlike condoms, HECs offer no protection against HIV. Dual-method use, or the use of condoms with HECs, is an ideal option to reduce HIV risk but is infrequently practiced. Rather, women tend not to use condoms when they use HECs and increase their HIV risk from their sexual partners. However, it remains unknown whether HIV status affects such tendency. Given the increasing popularity of HECs in sub-Saharan Africa, this study examined the association between the use of HECs and condom use among HIV-positive and negative women. Methods: A cross-sectional study was conducted among 833 sexually active women aged 18-49 years, recruited from six clinics in Siaya county, Kenya. From March to May 2017, female research assistants interviewed the women using a structured questionnaire. Multiple logistic regression analysis was conducted to examine the association between HEC use and consistent condom use in the past 90 days, adjusting for potential confounders. It was also examined with regular partners (husbands or live-in partners) and non-regular partners, separately. In addition, a sub-sample analysis of HIV-negative or unknown women was conducted. Results: In total, 735 women were available for the analysis. Among the women, 231 (31.4%) were HIV-positive. HIV-positive women were more likely to use HECs than HIV-negative or status unknown women (70.1% vs. 61.7%, p=0.027). HEC use was significantly associated with decreased condom use with a regular partner (adjusted odds ratio (AOR)=0.25; 95% CI 0.15-0.43, p<0.001) and a non-regular partner (AOR=0.25; 95% CI 0.11-0.58, p=0.001). However, compared with HIV-negative or status unknown women, HIV-positive women were more likely to use HECs and condoms consistently with a regular partner (AOR=6.54, 95% CI 2.15-20.00, p=0.001). Other factors significantly associated with consistent condom use included partner's positive attitude toward contraception, partner's HIV-positive status, high HIV risk perception, and desire for children in the future. Conclusion: Dual-method use was limited among HIV-negative women and women who had HIV-negative partners due to inconsistent condom use. The use of HECs was significantly associated with decreased condom use, regardless of partner type and their HIV status. Due to this inverse association, HIV-negative women may increase their HIV risk from their sexual partners. Therefore, interventions should be strengthened to reduce their dual risks of HIV infection and unintended pregnancy by promoting dual-method use. Family planning services should strengthen counseling on the possible risk of HIV infection from their sexual partners and target not only women but also their partners, who may play a key role in condom use.</p>
Data from: Contrasting patterns of population history and seed-mediated gene flow in two endemic Costa Rican oak species
Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in two partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. Phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.
Data from: In the shadows: phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)
The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity.
Data from: Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum
Well-characterised examples of homoploid hybrid speciation (HHS) are rare in nature yet they offer the potential to study a number of evolutionary processes. In this study we investigate putative homoploid hybrid species in the genus Argyranthemum (Asteraceae), a group of plants endemic to the Macaronesian archipelagos of the North Atlantic Ocean. We specifically address a number of knowledge gaps surrounding the origin(s) of A. sundingii and A. lemsii, which are thought to be derived from the same parental cross. Comparisons of leaf morphology suggest that A. sundingii and A. lemsii are distinct from their parental progenitors and distinguishable from each other based on leaf area. Ecological niche modelling (ENM) demonstrated that the homoploid hybrid species occupy novel habitats that are intermediate relative to the parental species. Nuclear SSRs and SNP data indicate that the homoploid hybrid species are distinct from the parental taxa, whilst population level sampling of chloroplast SSRs and Approximate Bayesian Computation show that A. sundingii and A. lemsii are independently derived from the same parental cross. As such, Argyranthemum represents an example of independent homoploid hybrid speciation events with evidence of divergence in leaf morphology and adaptation to novel intermediate habitats. On oceanic islands, which are often typified by steep ecological gradients and inhabited by recently derived species with weak reproductive barriers, multiple HHS events from the same parental cross are not only possible but are likely to have played a more important role in oceanic island radiations than we currently think.
Data from: Demographic history inferred from genome-wide data reveals two lineages of sheldgeese endemic to a glacial refugium in the southern Atlantic
Aim: The Malvinas/Falkland Islands (MFI) constitute the largest archipelago in the southern Atlantic, and harbour endemic lineages that presumably evolved after sea-level rise, associated with glacial periods, isolated ancestral populations. We investigate the role of the MFI in isolating populations from continental counterparts of two highly vagile species: the sheldgeese Chloephaga picta and Chloephaga rubidiceps. Location: Patagonia and the Malvinas/Falkland Islands. Methods: We sampled C. picta and C. rubidiceps on the continent and MFI. Using a reduced-representation genomic approach, we quantified the genetic differentiation between insular and continental populations of both species, and used coalescent-based analyses to model their demography. Results: The MFI harbour independently evolving lineages of C. picta and C. rubidiceps, which diverged from their continental counterparts during the Middle-Late Pleistocene and have since experienced negligible gene flow. Main conclusions: The c. 450 km that separate the archipelago from the continent are sufficient to isolate populations of these putatively highly vagile species. Ancestral lineages may have reached the MFI refugium during glacial cycles. Without conservation measures, the drastic decline of the morphologically, behaviourally and ecologically distinct continental population of C. rubidiceps, to < 1000 individuals, may lead to the extinction of an independently evolving taxon.
Data from: Oligocene–Neogene fossil history of Asian endemic conifer genera in Japan and Korea
Temporal and spatial changes of ten conifer genera that are endemic to East Asia were analyzed based on fossil data from humid temperate forests in the Japanese Islands and Korean Peninsula to elucidate the phytogeographic history, and to understand differences between those genera eliminated from the Japanese Islands and those remained extant. All these genera, except for Thujopsis, have existed in the area since the Paleogene and remained in the Japanese islands after initial separation from the continent at the early–middle Miocene. Those locally extinct six genera have tendencies to adapt to wider ranges of climatic conditions than their modern relatives. Metasequoia, Glyptostrobus, and Taiwania began to change their distributions since the late Miocene possibly through habitat partitioning. Keteleeria, Pseudolarix, and Cunninghamia appeared to have expanded their habitat toward warmer conditions during the mid-Miocene Climatic Optimum and then became restricted to warmer forest vegetation by the end of Pliocene. Overall changes in their distribution can be explained by climatic effects. On the contrary, three genera endemic to Japan (Sciadopitys, Cryptomeria, and Thujopsis) followed clearly different trends from the others. Cryptomeria and Thujopsis were especially adapted to cooler-temperate climate and they retained their habitat areas in the northern part of Japan. During the late Miocene–Pliocene, the islands connected with the Eurasian continent again, which probably acted as a corridor for warm-adapted genera to disperse southwest. Current data suggest that ecological requirements of each genus might be essential to decide whether they could survive on the Japanese Islands.
Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'
Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six nuclear loci and complete sampling for all known species. We use a time-calibrated Bayesian estimate of phylogeny and model-testing approach to biogeographic inference to infer ancestral areas and probable means of diversification. These analyses identify Sanguirana as an additional clade for which the biogeographic 'Out-of-Palawan' biogeographic scenario is unambiguously preferred. This study lends additional support to recent work suggesting that a substantial portion of Philippine vertebrate megadiversity originated via colonization of the archipelago from the Palawan microcontinent, with subsequent invasion of oceanic islands (e.g., range expansion over Huxley's Modification of Wallace's Line), numerous instances of overwater dispersal, and geographic radiation across the archipelago.
Data from: Post-Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow
Range expansions and gene flow as micro-evolutionary processes played a leading role in the population demographic history of marine organisms. Herein, we sequenced partial mtDNA Cox1 gene from 26 assigned geographic populations in order to understand how Irish moss (Chondrus crispus) responded to severe climatic oscillations during the Pleistocene glaciations and contemporary forces such as gene flow. Phylogeographic patterns indicated that haplotype frequency distributions were strongly skewed, with nearly half found only in single samples and thus restricted to a single population. Analysis of molecular variance revealed that most of the variation was within populations with no significant genetic structuring on either side of the Atlantic. Demographic analyses indicated that ISI (Irish Sea and Ireland) and NS (the North Sea) areas experienced a slight trend of increase in population size over time, whereas EC (the English Channel) area experienced expansion beginning approximately 170,000-360,000 BP. The observed complex genetic pattern of C. crispus is consistent with a scenario of multiple unrelated founding events by survival of this species in at least three putative Pleistocene refugia along the European coastline, and subsequent trans-Atlantic dispersal combined with contiguous northward population expansion predating the LGM and geographically gene flow.
Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)
AIM: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. RESULTS: Between five and eight genetically distinct lineages were identified that appear comparable to species with minimal or no hybridization. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (c. seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. MAIN CONCLUSIONS: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations.
Data from: Biogeography in a continental island: population structure of the relict endemic centipede Craterostigmus tasmanianus (Chilopoda, Craterostigmomorpha) in Tasmania using 16S rRNA and COI
We used 16S ribosomal RNA (rRNA) and cytochrome c oxidase subunit I (COI) sequence data to investigate the population structure in the centipede Craterostigmus tasmanianus Pocock, 1902 (Chilopoda: Craterostigmomorpha: Craterostigmidae) and to look for possible barriers to gene flow on the island of Tasmania, where C. tasmanianus is a widespread endemic. We first confirmed a molecular diagnostic character in 28S rRNA separating Tasmanian Craterostigmus from its sister species Craterostigmus crabilli (Edgecombe and Giribet 2008) in New Zealand and found no shared polymorphism in this marker for the 2 species. In Tasmania, analysis of molecular variance analysis showed little variation at the 16S rRNA and COI loci within populations (6% and 13%, respectively), but substantial variation (56% and 48%, respectively) among populations divided geographically into groups. We found no clear evidence of isolation by distance using a Mantel test. Bayesian clustering and gene network analysis both group the C. tasmanianus populations in patterns which are broadly concordant with previously known biogeographical divisions within Tasmania, but we did not find that genetic distance varied in a simple way across cluster boundaries. The coarse-scale geographical sampling on which this study was based should be followed in the future by sampling at a finer spatial scale and to investigate genetic structure within clusters and across cluster boundaries.
Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between the dominant model of rs877356 and binary TST status in the combined cohort (OR=0.2671, p=1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant rs2069885 had the most significant association (p=1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and T¬H2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected participants with extensive exposure increases the power to detect associations in complex infectious disease.
Data from: Phylogeny of seven Bulinus species originating from endemic areas in three African countries, in relation to the human blood fluke Schistosoma haematobium
Background: Snails species belonging to the genus Bulinus (Planorbidae) serve as intermediate host for flukes belonging to the genus Schistosoma (Digenea, Platyhelminthes). Despite its importance in the transmission of these parasites, the evolutionary history of this genus is still obscure. In the present study, we used the partial mitochondrial cytochrome oxidase subunit I (cox1) gene, and the nuclear ribosomal ITS, 18S and 28S genes to investigate the haplotype diversity and phylogeny of seven Bulinus species originating from three endemic countries in Africa (Cameroon, Senegal and Egypt). Results: The cox1 region showed much more variation than the ribosomal markers within Bulinus sequences. High levels of genetic diversity were detected at all loci in the seven studied species, with clear segregation between individuals and appearance of different haplotypes, even within same species from the same locality. Sequences clustered into two lineages; (A) groups Bulinus truncatus, B. tropicus, B. globosus and B. umbilicatus; while (B) groups B. forskalii, B. senegalensis and B. camerunensis. Interesting patterns emerge regarding schistosome susceptibility: Bulinus species with lower genetic diversity are predicted to have higher infection prevalence than those with greater diversity in host susceptibility. Conclusion: The results reported in this study are very important since a detailed understanding of the population genetic structure of Bulinus is essential to understand the epidemiology of many schistosome parasites.
Data from: Comparative genetic structure and demographic history in endemic Galápagos weevils
The challenge of maintaining genetic diversity within populations can be exacerbated for island endemics if they display population dynamics and behavioral attributes that expose them to genetic drift without the benefits of gene-flow. We assess patterns of genetic structure and demographic history in twenty seven populations of nine species of flightless endemic Galápagos weevils from nine of the islands and one winged introduced close relative. Analysis of mitochondrial DNA reveals significant population structure and moderately variable, though demographically stable, populations for lowland endemics (Fst= 0.094 to 0.541; π: 0.014 to 0.042; Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203), in contrast to signals of past contractions and expansions in highland specialists on two islands (Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203). We interpret this series of variable and highly structured population groups as a system of long-established independently founded island units, where structuring could be a signal of micro-allopatric differentiation due to patchy host plant distribution and poor dispersal abilities. We suggest that the severe reduction and subsequent increase of suitably moist habitat that accompanied past climatic variation could have contributed to the observed population fluctuations in highland specialists. We propose the future exploration of hybridization between the introduced and highland endemic species on Santa Cruz, especially given the expansion of the introduced species into the highlands, the sensitivity to past climatic variation detected in highland populations and the potentially threatened state of single-island endemics.
Data from: Geological and climatic changes in quaternary shaped the evolutionary history of Calibrachoa heterophylla, an endemic South-Atlantic species of petunia
Background: The glacial and interglacial cycles that characterized the Quaternary greatly affected the distribution and genetic diversity of plants. In the Neotropics, few phylogeographic studies have focused on coastal species outside of the Atlantic Rainforest. Climatic and sea level changes during the Quaternary played an important role in the evolutionary history of many organisms found in coastal regions. To contribute to a better understanding of plant evolution in this environment in Southern South America, we focused on Calibrachoa heterophylla (Solanaceae), an endemic and vulnerable wild petunia species from the South Atlantic Coastal Plain (SACP). Results: We assessed DNA sequences from two cpDNA intergenic spacers and analyzed them using a phylogeographic approach. The present phylogeographic study reveals the influence of complex geologic and climatic events on patterns of genetic diversification. The results indicate that C. heterophylla originated inland and subsequently colonized the SACP; the data show that the inland haplogroup is more ancient than the coastal one and that the inland was not affected by sea level changes in the Quaternary. The major diversification of C. heterophylla that occurred after 0.4 Myr was linked to sea level oscillations in the Quaternary, and any diversification that occurred before this time was obscured by marine transgressions that occurred before the coastal sand barrier's formation. Results of the Bayesian skyline plot showed a recent population expansion detected in C. heterophylla seems to be related to an increase in temperature and humidity that occurred at the beginning of the Holocene. Conclusions: The geographic clades have been formed when the coastal plain was deeply dissected by paleochannels and these correlate very well with the distributional limits of the clades. The four major sea transgressions formed a series of four sand barriers parallel to the coast that progressively increased the availability of coastal areas after the regressions and that may have promoted the geographic structuring of genetic diversity observed today. The recent population expansion for the entire species may be linked with the event of marine regression after the most recent sea transgression at ~5 kya.
Data from: The influence of selection on MHC DQA and DQB haplotypes in the endemic New Zealand Hector's and Māui dolphins
Strong balancing selection on the Major Histocompatibility Complex (MHC) can lead to different patterns in gene frequencies and neutral genomic variation within species. We investigated diversity and geographic structure of MHC genes DQA and DQB, as well as their inferred functional haplotypes, from two regional populations (East and West Coast) of the endangered Hector's dolphin (Cephalorhynchus hectori hectori) and the critically endangered Māui dolphin (Cephalorhynchus hectori maui) (West Coast, North Island), and contrasted these results with patterns from neutral microsatellites. The Māui had the lowest number of alleles for DQA (2) and DQB (3), consistent with strong genetic drift acting on this remnant population. However, the two retained DQA alleles are amongst the most divergent combinations of all four alleles found across the Hector's metapopulation, potentially reflecting the retention of divergent alleles due to balancing selection. The high frequency of the divergent DQB04 allele also gave this population the highest nucleotide diversity for DQB. Strong differentiation was evident for DQA, DQB, and DQA-DQB haplotypes between the regional populations of Hector's dolphins (FST>0.213) and both subspecies (FST>0.311). Differentiation was generally greater than observed at neutral microsatellite loci, suggesting the influence of selection between geographically proximate East and West Coast populations. This might be the result of spatial differences in directional selection on those opposite coastlines. Additionally, measures of the ratio of non-synonymous to synonymous substitutions (dN/dS) were consistent with balancing selection over evolutionary time. Together, these results suggest a complex interplay of balancing selection, directional selection, local fidelity, and genetic drift.
Data from: Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole
Glacial refugia protected and promoted biodiversity during the Pleistocene, not only at a broader scale, but also for many endemics that contracted and expanded their ranges within refugial areas. Understanding the evolutionary history of refugial endemics is especially important in the case of endangered species to recognise the origins of their genetic structure and thus produce better informed conservation practices. The Iberian Peninsula is an important European glacial refugium, rich in endemics of conservation concern, including small mammals, such as the Cabrera vole (Microtus cabrerae). This near-threatened rodent is characterised by an unusual suite of genetic, life history and ecological traits, being restricted to isolated geographic nuclei in fast-disappearing Mediterranean sub-humid herbaceous habitats. To reconstruct the evolutionary history of the Cabrera vole, we studied sequence variation at mitochondrial, autosomal and sex-linked loci, using invasive and noninvasive samples. Despite low overall mitochondrial and nuclear nucleotide diversities, we observed two main well-supported mitochondrial lineages, west and east. Phylogeographic modelling in the context of the Cabrera vole's detailed fossil record, supports a demographic scenario of isolation of two populations during the Last Glacial Maximum (LGM) from a single focus in the southern part of the Iberian Peninsula. In addition, our data suggests subsequent divergence within the east, and secondary contact and introgression of the expanding western population, during the late Holocene. This work emphasises that refugial endemics may have a phylogeographic history as rich as that of more widespread species, and conservation of such endemics includes the preservation of that genetic legacy.
Data from: Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera, Podarcis pityusensis (Squamata: Lacertidae)
Two monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time-calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This suggests a mid-late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089–0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present-day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.
Data from: A new species of logperch endemic to Tennessee (Percidae: Etheostomatinae: Percina)
Percina apina, the Tennessee Logperch, is described as a new species endemic to Tennessee and distributed in the Duck River system and Whiteoak Creek. The earliest collection records for Percina apina date to 1971 and the species was identified as Percina burtoni, the Blotchside Logperch. A phylogenetic analysis of mitochondrial DNA (mtDNA) published in 2006 showed that populations identified as Percina burtoni in the Duck River system and Whiteoak Creek were a new and undescribed species. In this study, we test the hypothesis that Percina burtoni is composed of multiple species through analyses of mtDNA, nuclear genetic variation, and traditional meristic trait morphology. Our analyses of morphological divergence, nuclear genotypes, mtDNA gene trees, and comparisons with other sister species pairs of logperches confirm the distinctiveness of Percina apina. Morphologically, Percina apina is distinguished from Percina burtoni through higher average numbers of lateral line scales (93.1 versus 89.9); pored lateral line scales (91.6 versus 88.8); rows of transverse scales (38.1 versus 33.6); and scales around the caudal peduncle (36.2 versus 33.5). The two species also differ in patterns of pigmentation; the lateral blotches in Percina apina are typically wider than high, whereas the blotches tend to be higher than wide in Percina burtoni. We recommend that future species descriptions of North American freshwater fishes leverage available genetic resources and include molecular phylogenetic assessments in analyses of taxon distinctiveness. In addition, we advocate the deposition of morphological data used in species descriptions to online data repositories to ensure that other researchers are able to evaluate and modify hypotheses of species delimitations.
Data from: Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae
Aim: To quantify taxon diversity, biogeographic distributions and patterns of community assembly in xeniid octocorals using molecular operational taxonomic units (MOTUs). Location Red Sea, Indian and western Pacific Oceans. Taxon Xeniidae, a family of reef-dwelling octocorals (Anthozoa, Octocorallia). Methods Xeniids collected at 13 locations were sequenced at three barcode loci, and assigned to molecular operational taxonomic units (MOTUs) defined by minimum genetic distance thresholds. Taxon richness (no. of MOTUs) and endemicity (percent of MOTUs found at a single location) were quantified. Patterns of β-diversity (species turnover) and phylogenetic β-diversity (lineage turnover) among geographical regions were visualized using hierarchical clustering, NMDS plots, and distance-decay relationships. Community assembly was investigated by comparing the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) separating species in each assemblage to values generated for null communities. Results A genetic distance threshold of 0.3% discriminated 67 MOTUs, with taxon richness ranging from 2-18 MOTUs per site. Out of the 67 MOTUs, 48 (72%) were found at only a single location, and only two spanned both the western Indian and Pacific Oceans. Species turnover among sites was high, but phylogenetic β-diversity was lower than β-diversity and differed significantly from null models of community assembly at only two sites. β-diversity and phylogenetic β-diversity both increased significantly with geographic distance, and sites clustered into three distinct biogeographic regions (Red Sea and western Indian Ocean; Western Australia; western Pacific and Great Barrier Reef, Australia). All five major clades of xeniids were represented in each region. Main Conclusions A genetic approach to biodiversity estimation suggests that most xeniid taxa are regional endemics whose geographic distribution is likely governed by dispersal limitation. This conclusion contrasts with published records of certain morphospecies occurrences, which imply that they have broad geographic ranges. So far, the distribution of xeniid biodiversity mirrors that of scleractinian corals, with species richness highest in the Coral Triangle, but endemicity peaking in peripheral areas.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.