Benthic habitats do show a significant latitudinal diversity gradient: A comment on Kinlock et al. (2018)

The latitudinal diversity gradient (LDG) has been investigated for decades, with hundreds of studies focusing on different organisms, regions and habitat types. Meta‐analysis may be considered, therefore, a useful tool to explore the generality and limitations of this remarkable macroecological pattern. The first meta‐analysis exploring variations in the LDG, published by Hillebrand in 2004, revealed that the latitudinal decline in species richness seems to be indeed a general phenomenon. However, Kinlock et al. (2018, Global Ecology and Biogeography, 27, 125–141) revisited recently the challenge of synthesizing individual LDGs and indicated that the phenomenon is not ubiquitous among habitats of the marine realm. More precisely, they indicated that the phenomenon is non‐significant in the benthic habitat. Here, we suggest that the marine habitat categories used by them (i.e., benthic, coral reefs, coastal, open ocean) are not independent and that reclassifying the studies significantly alters one of their main results. By assigning the studies into benthic and pelagic categories, and additionally into coastal or oceanic zones, we show that non‐ambiguous, evolutionarily meaningful marine habitats display a significant latitudinal decline in species richness.     

Overcoming the issue of small sample sizes in fragmentation genetics

Nazareno & Jump (2012) highlight potential issues with using small sample sizes in population genetic studies. By reanalysing allelic richness data from our recent publication on habitat fragmentation (Struebig et al. 2011), they assert that the observed relationship has been driven by three sites with the lowest number of individuals sampled. While sample size issues have been raised before in the genetic literature, Nazareno & Jump’s (2012) comment serves as a useful reminder to us all. Nevertheless, we disagree that our findings were significantly biased by sampling limitations. Here, we demonstrate by jackknifing that, contrary to the claims of Nazareno & Jump (2012), our correlations of allelic richness and fragment area are not driven solely by sites with low sample sizes. We maintain that small sample sizes can be accounted for in fragmentation studies and that sampling limitations should not detract from undertaking conservation genetic research.     

Striking case of convergence — Alleged marine gastropods in Cretaceous Burmese amber are terrestrial cyclophoroids. Comment on Yu et al.

Yu et al. (2019) recently described two new species of gastropods from the Cretaceous Burmese amber and attributed them to the marine family Epitoniidae. A close inspection of the images provided by Yu et al. indicates however that the species in question do not belong to that family or any marine gastropod group. In contrast, the two species are attributed here to the terrestrial operculate family Pupinidae (Cyclophoroidea) and tentatively to the genus Pseudopomatias. We briefly review the fossil record of the Cyclophoroidea and Pupinidae and discuss implications of the present revision. After all, Pseudopomatias? lyui (Yu, Wang and Jarzembowski, 2019) and P.? zhuoi (Yu, Wang and Jarzembowski, 2019) belong to the oldest members of the Pupinidae.     

Serious doubts over “Eggs forever?”

A recent commentary in this journal by Byskov et al. (2005) claims that, despite published results from numerous independent lines of investigation from our laboratory and others, there does not "exist any evidence for neo-folliculogenesis in the adult mammalian ovary." While we agree with Byskov et al. that our work represents a radical departure from the age-old dogma that mammalian females permanently lose the capacity for oocyte and follicle production during the perinatal period, careful examination of all of the available data leaves no doubt that adult female mammals retain the capacity for oogenesis and folliculogenesis. These findings do not change the fact that exhaustion of the oocyte pool occurs with advancing chronological age--a process responsible for driving the menopause in women--but rather question the basic mechanism underlying age-related ovarian failure. In this regard, studies of aging male mice have demonstrated that testicular atrophy is associated with a dramatic decline in the number, activity and quality of germline stem cells that maintain spermatogenesis during adulthood (Zhang et al., 2006). Therefore, to the contrary of the opinion of Byskov et al. that such a process would be "considered exceptional among stem cells," it is certainly reasonable to hypothesize that a similar deterioration of female germline stem cell function underlies the decline in oocyte quality and the onset of ovarian failure in aging females. Further, while we accept that a departure from conventional thinking can take years to gain widespread acceptance, we feel this resistance to change should not be construed as the sole means to voice opinions about the validity of our data or the maturity of our principal conclusion.     

Commentary on Coram et al. (2021) on the use of Facebook to understand marine mammal stranding issues in Southeast Asia

We reviewed Coram et al. (Biodivers Conserv 30:2341–2359, 2021, https://doi.org/10.1007/s10531-021-02196-6), a paper that highlights the use of social media data to understand marine litter and marine mammals in Southeast Asia. While we commend its intent, we find that the methodology used and conclusions drawn portray an incomplete and inaccurate perception of how strandings, stranding response, and analysis of stranding data have been conducted in the region. By focusing on investigative results revealed by a very limited search of one social media platform (Facebook), using only English keywords, and insufficient ground-truthing, Coram et al. (2021) have, unintentionally, given the perception that Southeast Asian scientists have not conducted even the bare minimum of investigation required to better understand the issue of marine litter and its impact on marine mammals. In this commentary we provide a more accurate account of strandings research in Asia and include recommendations to improve future studies using social media to assess conservation issues.

     

Brief communication: human cranial variation fits iterative founder effect model with African origin

Recent studies comparing craniometric and neutral genetic affinity matrices have concluded that, on average, human cranial variation fits a model of neutral expectation. While human craniometric and genetic data fit a model of isolation by geographic distance, it is not yet clear whether this is due to geographically mediated gene flow or human dispersal events. Recently, human genetic data have been shown to fit an iterative founder effect model of dispersal with an African origin, in line with the out-of-Africa replacement model for modern human origins, and Manica et al. (Nature 448 (2007) 346-349) have demonstrated that human craniometric data also fit this model. However, in contrast with the neutral model of cranial evolution suggested by previous studies, Manica et al. (2007) made the a priori assumption that cranial form has been subject to climatically driven natural selection and therefore correct for climate prior to conducting their analyses. Here we employ a modified theoretical and methodological approach to test whether human cranial variability fits the iterative founder effect model. In contrast with Manica et al. (2007) we employ size-adjusted craniometric variables, since climatic factors such as temperature have been shown to correlate with aspects of cranial size. Despite these differences, we obtain similar results to those of Manica et al. (2007), with up to 26% of global within-population craniometric variation being explained by geographic distance from sub-Saharan Africa. Comparative analyses using non-African origins do not yield significant results. The implications of these results are discussed in the light of the modern human origins debate.     

A comparative study of asymmetric migration events across a marine biogeographic boundary

In many nonclonal, benthic marine species, geographic distribution is mediated by the dispersal of their larvae. The dispersal and recruitment of marine larvae may be limited by temperature gradients that can affect mortality or by ocean currents that can directly affect the movements of pelagic larvae. We focus on Point Conception, a well-known biogeographic boundary between the Californian and Oregonian biogeographic provinces, to investigate whether ocean currents affect patterns of gene flow in intertidal marine invertebrates. The predominance of pelagically dispersing species with northern range limits at Point Conception suggests that ocean currents can affect species distributions by erecting barriers to the dispersal of planktonic larvae. In this paper, we investigate whether the predominantly southward currents have left a recognizable genetic signature in species with pelagically dispersing larvae whose ranges span Point Conception. We use patterns of genetic diversity and a new method for inferring cladistic migration events to test the hypothesis that southward currents increase southward gene flow for species with pelagically dispersing larvae. We collected mitochondrial DNA (mtDNA) sequence data for the barnacles Balanus glandula and Chthamalus fissus and also reanalyzed a previously published mtDNA dataset (Strongylocentrotus purpuratus, Edmands et al. 1996). For all three species, our cladistic approach identified an excess of southward migration events across Point Conception. In data from a fourth species with nondispersing larvae (Nucella emarginata, Marko 1998), our method suggests that ocean currents have not played a role in generating genetic structure.     

Sinoatrial node pacemaker cells:cardiomyocyte-or neuron-like cells?

The sinoatrial node(SAN)is the headquarter of heartbeat throughout our lifetime(Lakatta et al.,2010;Cingolani et al.,2018;Peters et al.,2020).Every beat of the heart is triggered by a bioelectric pulse spontaneously released by SAN pacemaker cells(SANPCs)(Yaniv et al.,2014;Yavari et al.,2017).In adult human heart,the SAN is a crescent-shaped structure of 1-2 cm long and 0.5 cm wide,which is located at the junction of the superior vena cava and the right atrium and lies along the sulcus terminalis(John et al.,2016).However,the nature of SANPCs remains incompletely known.In general,SANPCs have long been considered as specialized cardiomyocytes(Van Eif et al.,2018;Linscheid et al.,2019;Galang et al.,2020;).However,SANPCs do not have myofibril and T-tube,thus not sharing the contractility property of cardiomyocytes(Satoh,2003;Protze et al.,2017).Interestingly,SANPCs share some electrophysiolog-ical characteristics with neurons:excitability and conductiv-ity.In addition,SANPCs have their intrinsic autonomic rhythm,while neurons also possess the intrinsic ability to generate spontaneous electrical impulses(Lisman et al.,2018).Whether SANPCs are neuron-like cells that reside in the heart remains enigmatic in the field.     

南中国海野生海水鱼类外寄生车轮虫新记录

研究对采自南中国海的7种海水鱼类进行了调查研究, 并分离获得4种隶属于车轮虫属的种类,分别为浦氏车轮虫Trichodina puytoraci Lom, 1962; 日本车轮虫Trichodina japonica Imai, et al., 1991; 直钩车轮虫Trichodina rectuncinata Raabe, 1958 与鲀车轮虫Trichodina fugu Imai, et al., 1997。研究发现鲀车轮虫Trichodina fugu Imai, et al., 1997为寄主鱼虫纹东方鲀Takifugu vermicularis的病原, 且能在野生条件下将其致死。上述4种车轮虫的形态分类学数据均基于干银法标本获得。研究是对我国南中国海车轮虫的首次报道。       

Low-Density Granulocytes Are Elevated in Mycobacterial Infection and Associated with the Severity of Tuberculosis

Tuberculosis remains a global health problem caused by infection with Mycobacterium tuberculosis. Numerous studies have established a close correlation between the development of tuberculosis and the roles of neutrophils. Recently, a distinct population of CD15⁺ granulocytes was found to be present in the peripheral blood mononuclear cell (PBMC) fraction in humans. This population of granulocytes, termed low-density granulocytes (LDGs), was reported to be elevated and associated with disease activity or severity in a number of different conditions including SLE, asthma and HIV infection. However, both the frequency and clinical significance of LDGs associated with tuberculosis are unclear. Here we determined LDG levels and made comparisons between subjects with active pulmonary tuberculosis (PTB) and healthy controls, between PTB patients with mild-to-moderate disease and patients with advanced disease, and among PTB patients following anti-tuberculous therapy of varying durations. The direct correlation between M. tuberculosis infection and LDG levels was confirmed by in vitro infection of whole peripheral blood and isolated granulocytes with mycobacteria. Our results demonstrated that PBMCs in PTB patients contained significantly elevated percentages of LDGs compared with control subjects. LDGs in tuberculosis expressed higher levels of activation markers compared to normal-density granulocytes (NDGs). M. tuberculosis induced the generation of LDGs in both whole blood and isolated NDGs from control subjects, which suggests that LDGs associated with M. tuberculosis infection are likely to originate from in situ activation. Furthermore, our results revealed that the frequency of LDGs is associated with the severity of tuberculosis.     

Confounding social and mating systems predictably lead to biased results when examining the evolution of cooperative breeding in cichlids: A response to Tanaka et al.

In 2017, we demonstrated that transitions to cooperative breeding in Lamprologine cichlid fishes were not related to a species’ social mating system (Dey et al. 2017. Nature Ecology & Evolution, 1 , 137). This contrasted previous evidence that monogamy (and a low degree of promiscuity) promoted transitions to cooperative breeding in other taxa. Recently, Tanaka et al. (2018. Ethology, 124 , 777–789) critiqued our study and argued that a re‐analysis of the data shows transitions to cooperative breeding are promoted by non‐monogamous mating systems. Here, we show that Tanaka et al.'s critique contains numerous inaccuracies. In addition, we show that the results put forth by Tanaka et al. emerge only under the extreme scenario in which all cooperative breeding species are classified as non‐monogamous, which we argue arises because Tanaka et al. confound social systems and mating systems. While we agree that there is uncertainty regarding the mating system of some Lamprologine species, we argue this uncertainty was sufficiently addressed through the extensive sensitivity analyses conducted in our original study.     

Characterization of a Novel Population of Low-Density Granulocytes Associated with Disease Severity in HIV-1 Infection

The mechanisms resulting in progressive immune dysfunction during the chronic phase of HIV infection are not fully understood. We have previously shown that arginase, an enzyme with potent immunosuppressive properties, is increased in HIV seropositive (HIV+) patients with low CD4⁺ T cell counts. Here we show that the cells expressing arginase in peripheral blood mononuclear cells of HIV+ patients are low-density granulocytes (LDGs) and that whereas these cells have a similar morphology to normal-density granulocyte, they are phenotypically different. Importantly, our results reveal that increased frequencies of LDGs correlate with disease severity in HIV+ patients.     

Noise does not equal bias in assessing the evolutionary history of the angiosperm flora of China: A response to Qian (2019)

In response to our paper on the evolutionary history of the Chinese flora, Qian suggests that certain features of the divergence time estimation employed might have led to biased conclusions in Lu et al (2018). Here, we consider Qian's specific criticisms, explore the extent of uncertainty in the data and demonstrate that (i) no systematic bias toward dates that are too young or too old is detected in Lu et al.; (ii) constraint of the crown age of angiosperms does not bias the generic ages estimated by Lu et al.; and (iii) ages derived from the Chinese regional phylogeny do not bias the conclusions reported by Lu et al. All these analyses confirm that the conclusions reported previously are robust. We argue that, like many large-scale biodiversity analyses, sources of noise in divergence time estimation are to be expected, but these should not be confused with bias.     

Testing the level of ant activity associated with quorum sensing: an empirical approach leading to the establishment and test of a null-model (response to the comment of Richardson et al.)

In a paper in this journal (Nouvellet et al., 2010), we presented results from experiments on the behaviour of the Pharaoh's ant, Monomorium pharaonis, along with a substantial statistical and theoretical analysis of the results. In a minor part of our paper, we compared our results with the related work of Richardson et al. (2010a). These authors have subsequently commented on our interpretation of their work (Richardson et al., 2011). In this Letter we respond to the comments of Richardson et al. (2011), and give detailed arguments why we stand by our original conclusions.     

Fish ACE2 is not susceptible to SARS-CoV-2

The ongoing pandemic of coronavirus disease 2019 (COVID-19) has reshaped our daily life and caused > 4 million deaths worldwide (https://covid19.who.int/). Although lockdown and vaccination have improved the situation in many countries, imported cases and sporadic outbreaks pose a constant stress to the prevention and control of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent responsible for COVID-19, has a positive-sense single-stranded RNA genome of 30 kb (Coronaviridae Study Group of the International Committee on Taxonomy of Viruses, 2020). We and other groups have demonstrated that the SARS-CoV-2 could use the angiotensin-converting enzyme 2 (ACE2) as cell receptor, including orthologs of a broad range of animal species such as human, bats, ferrets, pigs, cats, and dogs (Hoffmann et al., 2020; Zhou et al., 2020; Liu et al., 2021). Although the evolutionary origin of SARS-CoV-2 can be linked to the discoveries of diverse coronaviruses related to SARS-CoV-2 in wild animals such as bats (Zhou et al., 2020; Wacharapluesadee et al., 2021) and pangolins (Liu et al., 2019; Lam et al., 2020), the direct origin of SARS-CoV-2 in humans remains unknown. In China, several sporadic outbreaks of COVID-19 in 2020 were linked to food in cold chain sold at trade markets, including salmon meat (http://www.nhc.gov.cn/xcs/yqtb/list_gzbd.shtml) (Yang et al., 2020). The detection of SARS-CoV-2 RNA on the surface of frozen meat for as long as 20 days has also been reported (Feng et al., 2021). A concern regarding the potential role of fish in SARS-CoV-2 transmission has also been raised. Therefore, we investigated the susceptibility of fish ACE2 to SARS-CoV-2.     

Yes,correct context is indeed the key: An answer to Haave‐Audet et al. 2019

We published a study recently testing the link between brain size and behavioural plasticity using brain size selected guppy (Poecilia reticulata) lines (2019, Journal of Evolutionary Biology, 32, 218‐226). Only large‐brained fish showed habituation to a new, but actually harmless environment perceived as risky, by increasing movement activity over the 20‐day observation period. We concluded that “Our results suggest that brain size likely explains some of the variation in behavioural plasticity found at the intraspecific level”. In a commentary published in the same journal, Haave‐Audet et al. challenged the main message of our study, stating that (a) relative brain size is not a suitable proxy for cognitive ability and (b) habituation measured by us is likely not adaptive and costly. In our response, we first show that a decade's work has proven repeatedly that relative brain size is indeed positively linked to cognitive performance in our model system. Second, we discuss how switching from stressed to unstressed behaviour in stressful situations without real risk is likely adaptive. Finally, we point out that the main cost of behavioural plasticity in our case is the development and maintenance of the neural system needed for information processing, and not the expression of plasticity. We hope that our discussion with Haave‐Audet et al. helps clarifying some central issues in this emerging research field.     

GC3 heterogeneity and body temperature in vertebrates

A recent paper by Belle et al. (J. Mol. Evol. 55 (2002) 356) reported an analysis of mean GC(3) (the GC level of third codon positions) and standard deviations of GC(3) of vertebrate genomes as related to body temperature, and concluded that "the thermal stability hypothesis does not appear to explain the general patterns of composition", apparently contradicting a previous working hypothesis from our laboratory. We have analyzed the data of Belle et al. and find that their data not only do not contradict the thermal stability hypothesis, but if anything support it.     

Characterization of low-density granulocytes in COVID-19

Severe COVID-19 is characterized by extensive pulmonary complications, to which host immune responses are believed to play a role. As the major arm of innate immunity, neutrophils are one of the first cells recruited to the site of infection where their excessive activation can contribute to lung pathology. Low-density granulocytes (LDGs) are circulating neutrophils, whose numbers increase in some autoimmune diseases and cancer, but are poorly characterized in acute viral infections. Using flow cytometry, we detected a significant increase of LDGs in the blood of acute COVID-19 patients, compared to healthy controls. Based on their surface marker expression, COVID-19-related LDGs exhibit four different populations, which display distinctive stages of granulocytic development and most likely reflect emergency myelopoiesis. Moreover, COVID-19 LDGs show a link with an elevated recruitment and activation of neutrophils. Functional assays demonstrated the immunosuppressive capacities of these cells, which might contribute to impaired lymphocyte responses during acute disease. Taken together, our data confirms a significant granulocyte activation during COVID-19 and suggests that granulocytes of lower density play a role in disease progression.