Biogeography - Science topic

Are you interested in joining our Juglandaceae-network?

We are working on global biogeography and conservation of the relict tree family Juglandaceae. However, the distribution and status knowledge of many species of South-Eastern Asia are not well known.

We are searching therefore for local experts of Engelhardia apoensis. According to our knowledge, the species is present in continental Malaysia, Borneo, Brunei, Philippines. Please see the attached schematic map with known distribution (administrative units & countries).

Any information, maps, publications, reports, personal observations, etc. from your region are interesting for us.

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP.

Could someone please help me review these steps and results?

Thank you!

I submitted a manuscript to the Journal of Biogeography. It has been 7 months and it still under review. I am just wondering if anyone else here has had a similar experience and how long it was before it was accepted. TIA.

Physical geography is includes the study of the earth spheres. Geographers usually working on geomorphology, climatology and biogeography. Why they don't work mostly in oceanography ?

Discussion.

Just about everyone these days uses fossils to calibrate molecular divergence. Fossils only provide minimum ages, but these are magically transmogrified into actual or maximal dates that are supposed to falsify earlier origins supported by tectonic methods. Ancestral area analysis can generate chance dispersal for patterns that could just as well be the result of vicariance. Ancestral area analysis uses areas that have no emperical existence. Its all a bit like following Alice down the rabbit hole. Numbers or not, nonsense is still nonsense.

According to distribution maps (IUCN, http://www.iucnredlist.org/details/183882/0) this species has been restrictively allocated to specific sites in the eastern Pacific including the Gulf of California (Mexico), Cocos Island National Park (Costa Rica), Galapagos (Ecuador) and Lobos de Afuera Island (Peru). I was wondering if there is any other unofficial/unpublished report for H. fossatus in the eastern Pacific

Biogeography theory predicts that species will either migrate, adapt, or go extint under environmental change. Due to limited mobility in plants, their options are limited to adaptation, including phenological changes, which has been observed for many plants. So, do we have adequate data to be able to identify traits that confer plants the ability to shift their regeneration or flowering phenologies due to climate change? Could you please mention those traits and provide links to papers with empirical evidence. Thank you!

That's probably a beginner question, but, after I run the BBM analysis and go to the graphic tree view how interpretation I give to the symbols in event matrix on Information tab? An example:

NODE93:

EVENT MATRIX:

Dispersal:2

Vicariance:1

Extinction:0

Event Route:

->^C->C^C->C|C

PROBABILITY:

0.0000

 What's mean the numbers in Dispersal, Vicariance and Extinction? And the simbols in event route between the area C, they have the same significance which have in mathemarical equations?

Please, help me to figure out with the next situation: there are two alien species in the flora of a country, they are parental ones for a hybrid which was described and is known only from a few locations within this country. Could I say that this hybrid is native to this country?

    My research topic is to explore the biogeograpgic patterns of species richness of insects. I have the regional richness data of all insects and different orders from many locations. It's well known that insects include c. 30 orders with different numbers of species and phylogenies. I want to group different insect orders into several groups, and make a clear description of their diversity patterns. The problem is in grouping different insect orders into several groups.

    I'm also looking for someone interested in this project. Please contact me if you want to join me. 

My nuclear and cpDNA are incongruent, and We keep them separate. I would like to do biogeography analyses. Which kid of trees, nuclear or cpDNA, are prefered for this analysis and why?

Hello! I've recently come across the need to reproject some environmental raster layers from the mercator projection into an area-conserving projection: cylindrical equal area.

Reprojecting in R using the projectRaster function, then writing the rasters as tif files, I'm getting files that are significantly large so that I quickly run off of usable computer space in my analysis (I have approximately 50 environmental rasters).

My question is: is there a way to avoid this significant file size increase? It could be either through saving the reprojected raster in another format that is more lightweight; another equal area projection that through reprojection from mercator leads to lesser distortion/size increase;

Thank you in advance for any input!

I am researching the geographical distribution of the most common cosmopolitan springtail species. Can you recommend sources related to collembola phylogeography?. It would be nice if we collected a significant number of references on this issue.

I am looking for information on current records of free-ranging European wild boar (Sus scrofa) in Mexico. If you have information help me. Thank you!

Hello. My name is Malte. In my master thesis I study assemblages of Meso and Makrofauna associated with arboreal soil in tree-cavities, following an approach of island biogeography. In my study design the two predictors "size of tree cavity (amount of arboreal soil)" and "isolation (distance between tree cavity and terrestrial ground)" are included. Taking samples of twelve trees - sampling 1 tree cavity per each tree, 2 surveys with one year inbetween were conducted, including the following steps: Removal of arboreal soil of tree-cavities, Extraction of Fauna, Sterilization and restoration of arboreal soil into tree-cavities. I determined taxonomic groups to order level and counted the individuals. Having my dataset complete, the first thing I want to look at, analyzing my data, is the occurence probability of the insular groups (those that are bound to the arboreal soil in tree-cavities, e.g. Crassiclitellata) as a function of the predictors described above. I want to perform a zero-inflated regression model as it can consider the two distinct stochastic processes - 1. Colonization and 2. Abundace > 0 (Kéry and Royle 2015).

I'm looking at using genomic data to do some biogeographic research. Are there any databases that could be used in geospatial analysis?

Burlap traps are a way to mitigate the invasive Lymantria dispar dispar (tussock/gypsy moth) caterpillars, which defoliate mainly hardwood deciduous trees. Burlap is wrapped around trees and tied with twine, then folded to create a flap and ideal conditions where the caterpillars migrate into. The caterpillars are then disposed of in soapy water when the traps are checked.

If I want to study spatial ecology of these caterpillars, using quantitative analysis from each trap at a small lake surrounded by forest, how should I prioritize trap set-up (location, amount)?

Should the traps be completely randomized?

My study area is at maximum 2 square kilometres with a small Lake taking up about 0.25 of those square km.

Ideally I want to minimize confounding variables such as tree species the traps are placed on.

The goal of this project is to determine spatial distribution of the caterpillars and to mitigate them with weekly checks.

Any help would be greatly appreciated!

I evaluated the contribution of deterministic factors on my bacterial communities, however, I also would like to quantify or estimate the effect of potential stochastic processes that might explain the remaining variation unexplained under environmental conditions.

From your viewpoint, what are the future main challenges in studying Biomes, Biogeography, Terrestrial & Aquatic Ecosystems of the World?

Best regards,

Saeed

Earth have diverse group of insects, if a species of insect got extinct, how we can assess and identify them? What are the criteria’s to follow?

Herewith I am sharing Call for papers for the 4th volume of the series “Biodiversity, biogeography and nature conservation in Wallacea and New Guinea”. Manuscripts on zoology, botany, ecology & nature conservation are welcome.

Attached: „Call for papers iv.pdf” (ca. 85 KB), „instructions.pdf“ (ca 62 KB).

KK

I aim to do a PhD in the future (on the general topic of ecology and biogeography) and would like to do a masters before this to make myself a more competitive candidate. However, I am pretty stuck on whether an MRes on a relevant topic or a skills based MSc (in Remote Sensing and GIS) would be a better option?

Let us consider a set of fossil occurrences of the same lineage in two separated geographic spaces (e. g., two landmasses, two hydrographic basins, two ocean basins).

Given such dataset, would it be possible to use the time intervals of fossil occurrences to calculate dispersal time estimates, or the earliest occurrence of the lineage in the geographic space to which it has dispersed? What would be the best method to use?

Hi All,

Are you an expertise in getting ancient DNA? Currently I am looking researchers who have expertise in getting DNA from old herbaria collections. Even better if you have it with Ascomycota (Fungi). If so and you like to collaborate with taxonomist to work in projects about systematics, evolution and biogeography, please contact me at lquijull@gmail.com or luis_quijada@fas.harvard.edu and write in the subject of the email "ancient DNA". I am looking for collaboration to learn these technics but also you will be coauthor of the results of this project that start in July.

Best wishes

Luis

I am currently looking for Invasive Alien Plant Species (IAPS) Occurrence-Data for mainly the Tropics including Africa, South America, & Asia tropical regions. If you know any research-networks or sources (published and/or Unpublished) of this data, please point me to it. The data would be mainly used for IAPS - Species Distribution Modelling.

NB: I have already gone through most of the data from International Databases (e.g.GBIF and GISD), however.. it is abit lacking.

I thank you in advance for your responses.

Sincerely,

NM

Do you have any suggestions regarding good computer software or programs for a systematic review? I am new to this type of research, can you please guide me in doing such? The topic would focus on biogeography/ecology.

Thank you very much.

I am working on a biogeographic study, in which to assess the latitudinal diversity gradient of amphibians in the Malay Peninsula. Thus, I’m required to examine the effects of utilizing different distribution data such as IUCN range maps, GBIF, modeled distribution, and a combination of those data, in mapping species richness in the Malay Peninsula.

My question is, what kind of statistical analysis that is suitable to compare the performances of these different distribution data in mapping species richness?

I am looking for current bibliography (books, articles...) about biogeography, specially about oceans, marine paleogeography and marine biodiversity patterns of distribution

Do any Caytonia-type cupules exceed one centimeter in greatest dimension?

Dear all,

I am stuck with a non-significant quadratic regression model (see attachment). The independent variable is altitude, whereas the dependent/response variable is species richness (count data). I have tried to log-transform the independent variable but p value is still greater than 0.05.

I am studying the elevational pattern of plant species richness. Simple count of species along the elevation leads to a ‘hump-shaped pattern of species richness’. Part of my methods is to generate a quadratic model of this pattern.

Is it worth to publish this research even though the quadratic model is insignificant? Do I have other alternatives? Please advise.

Thank you,

Faiz

mutation in biogeography based optimization differs from genetic algorithm?

In the urgent need to obtain reliable information quickly for the development of effective conservation plans, it is very useful to be able to combine tools from other disciplines to detect patterns and gaps in the information. I would appreciate if you can share your opinions and experiences!

Dear colleagues,

a MaxEnt model of the present distribution of a South American spider species based on 30 collection points (crossvalidated by running 30 replicates, regularization multiplier 0.5 and 1000 maximum iterations) resulted in an average test AUC ˂ 0.7, which is considered too low for further use (Swets, 1988).

Apart from the question if the AUC is suitable to measure the models performance (Lobo et al. 2008), could it be that there is a biological reason for the low AUC? E.g. that the used abiotic variables are not as important as for other species or that we are dealing with two separate species? If so, wouldn't it be advisable to discuss this model anyway, despite the low AUC?

Your opinion or reference to existing literature would be highly appreciated.

Best regards, Robert

I am working with biogeography of southern Paraguay and the info about Paraguay river evolution is relevant for my work. So, if someone could help me, I will be very gratefull! Specially, I have not any info about the Center and South Paraguay river evolution. Brazilian Pantanal and Formosa, Argentina, have information I already get, but nothing about paraguayan sections of actual river course.

Thanks

Are you interested in joining our Juglandaceae-network?

We are working on global biogeography and conservation of the relict tree family Juglandaceae. However, the distribution and status knowledge of many species of Meso- and South America are not well known.

We are searching therefore for local experts of Oreomunnea mexicana. According to our knowledge, the species is present in Mexico, Nicaragua, Costa Rica and Panama. The indications from Colombia need revision. Please see the attached schematic map with known distribution (administrative units & countries).

Any information, maps, publications, reports, personal observations, etc. from your region are interesting for us.

Trees don’t grow in deserts (e.g., Sahara). Why? – The answer to this question is based on a particular combination of evolutionary history, physiology and ecology.

Do you agree with this statement?

Could you explain your point of view?

[I’m a Brazilian biologist and writer. I write about science (mainly about population biology) and would like to know the opinion of colleagues from any field of scientific knowledge (and from other countries).]

See also Habitat, environment and ecological niche (https://www.researchgate.net/post/Habitat_environment_and_ecological_niche).

At this very moment (2 September; 22h00, local time), the National Museum (MN, Rio de Janeiro, Brazil), one of the most important museums of natural history in the world, is burning in flames.

In addition to the exhibitions open to the public, the MN housed some of the largest and most important scientific collections existing in Brazil. The collections of biological items included thousands of types (insects, reptiles, birds, mammals, plants, etc.).

To the taxonomists (and other colleagues): You could say how many specimens (mainly types) collected or described by you were deposited in MN? And to what taxonomic groups (family or above) these specimens belonged?

[In 2016, a coup d’état turned Brazil in a country with no future. Now, in his final months at the head of the Government, the President Michel Temer wants also to ensure that the country erase its own past.]

Habitat, environment and ecological niche are three distinct concepts.

Do you agree with this statement?

Could you explain your point of view?

[I’m a Brazilian biologist and writer. I write about science (mainly about population biology) and would like to know the opinion of colleagues from any field of scientific knowledge (and from other countries).]

See also Evolution, Darwinism and selection (https://www.researchgate.net/post/Evolution_Darwinism_and_selection).

I have been studying on Anatolian ground squirrel for about 20 years. For a while, I have also been interested in the ENM aprroach. Across its geographic distribution, I have been collecting tissue samples every about 20-40 km, and, in the meantime, occurrence records. So, I need a standard method to quantify number of populations (of occupied patches) to associate that measure with suitability obtained by ENM approach. It is difficult for me to quantify population density in a patch because I do field studies across the range. But, I have an observation that frequency of observation (encountering with an individual) tends to be high in areas of high suitability while travelling and collecting tissue samples across a region. That is, the methodology should be compatible with that I am travelling and collecting tissue samples and occurrence records across 100-200 km every day. Note that frequency of observation is also associated with time of day and season!

Analysing morphology-habitat relationships in a montane plant species, I am thinking of using slope exposition (i.e., northern, southern slopes, etc.) as one of the habitat features, since a direct measuring of all the associated microclimatic factors appears problematic. I have plant samples from many sites within a montane area of ca. 1300 squared kilometres and for each site I have slope sexposition data (cardinal and inter-cardinal directions). I need to correlate this data with leaf morphometric anatomical/morphological traits.

I would be grateful if someone could also recommend some papers reporting relationships between plant growth/occurrence and slope exposition in mountains.

Ecological niche modeling is increasingly important for understanding the factors that shape species distributions, as well as testing biogeographical hypotheses about species past, present, and future distributions as well as the role of ecology in speciation. However, most niche modeling work has focused on terrestrial and marine species (sound like conservation biology, in general?). I have previously used MAXENT to develop and project models of fish distributions, and the models we have published exhibited excellent predictive performance. And I am very interested in continuing to do so, particularly through coupling ENMs with phylogeographic analyses, and/or using them to inform phylogeographic hypotheses testing. However, I am skeptical of all models to some degree, and I am wanting to learn whether other techniques exist that would be more suitable for freshwater fish ecological niche modeling and paleoclimatic modeling, other than MAXENT (which is obviously most convenient for me). I am also interested in what the best data layers are for ENM analyses of freshwater habitats. I always want to learn more about these topics, so I figured I would ask here.

So, first, do such 'better' ENM models exist that could/should be used instead of or in combination with MAXENT? And, if so, what is required to run such other models, and how would the assumptions of these potentially 'better' models differ from those of MAXENT in different cases?

Second, it seems that a limitation of ecological niche modeling for freshwater taxa is a lack of sufficiently high resolution data layers for aquatic habitats. However, I am unsure about geospatial data repositories or resources for generating more suitable layers, and I would like specific advice about GIS procedures and data layers for making better data coverages. I am aware that some people are already doing this, but usually at very fine spatial scales. The broader community of ecologists and evolutionary biologists interested in fishes would therefore benefit much more from more comprehensive coverages.

FYI, I should indicate that I am not really interested in using masks over bioclimatic variables to restrict model output to the boundaries of stream and river networks, because many pilot analyses I have run on North American species suggest this does not add much or produce different results relative to running the models without such masks. So, I would prefer to avoid such discussion unless you know or can show me that doing so improves model performance. Thanks in advance for your replies. Take care.

Do the Satpura hypothesis, Brij Hypothesis stands good for this ecological puzzle

Dear colleagues, herein some points that I would like some discussion and, if possible, some answers in regards to global fungal richness estimates:

The question of how many species of Fungi there are has occasioned much speculation, as said Dr. D. Hawksworth and Dr. R. Lücking, but the estimatives, in many cases are too big!

Do we have any estimates of the species richness of all fungi for the neotropical region?

And what is the most up-to-date estimate for fungal species richness globally?

Is it possible to determine how much of this corresponds to soil mycobiota?

How sensitive are the methods of estimating fungal richness?

Attached, some useful papers:

HAWKSWORTH (2012) and HAWKSWORTH & LÜCKING (2017)

I'm looking for community-level datasets older than 20 years, at the landscape spatial-scale (i.e. multiple survey points in space), for any taxa or region.

If you know any dataset with these characteristics, please list it in the answers (hopefully with a related reference or website).

Thank a lot for your help,

All the best for 2018!

Cheers,

David.-

What were the general inferences concluded after the phylogeny reconstruction?

I tried searching for full text of this book but ended up with only 2-3 pages book reviews.

Dear all!

Could you recomend me program which demonstrate a distribution of species? especcialy rare ones? I have some data connecting with occure populations of species in region and would like create a maps. Thanks in advance!

Are there any evidences of anthropochorous origin of some Erinaceidae populations in the continental areas?

Are there also any evidences, in some populations, of recent expansion in the distribution area?

Thanks

Armando

I am looking for help finding clear and relatively certain material about the when and where of the migrations of haplogroup h, including any details about the cultures, the climates, and the geography. Thank you.

Good day

I am doing a study on landscape genetics at a fine-scale and need to use the program GESTE however I'm struggling to create the factor input file.

Can anybody please help me with this?

Landscape history of Dehesa Montado.

Dear all

I try to do a simultaneous autoregressive (SAR) models to take the spatial correlation into account (Kissling & Carl, 2008). I already selected the best combinations of weight list and neighbours distance by using the value of AIC and minRSA. But I have problem on how to calculate the relative importance of each predictor, especially on calculating the model fit using pseudo-R2 (Pearson correlation of observed and predicted values) and Akaike weights (w). 

<SAR models were run for all possible subsets of the five predictor variables (n = 32 models) under a multi-model inference approach. For each subset model, an Akaike’s information criterion (AIC) score was calculated and used to select the most parsimonious model (Akaike, 1987) and model fit was assessed using pseudo-R2 (Pearson correlation of observed and predicted values). The relative importance of each climate and soil variable for explaining mean range size variation was determined by summing the Akaike weights (w) across all models containing the target variable> a method in Rachael V. Gallagher Journal of Biogeography (J. Biogeogr.) (2016) 43, 1287–1298

Can anyone give some suggestions on how to do the above analysis?

Thanks

to detect the factors that accelerate the occurrence of rigor mortis

Coecobrya tenebricosa is a small collembolan species noted at least from North America and Europe (data eg. from www.gbif.org). The species was described from USA (Washington D.C.) but actually is known also from at least a few Europen countries. I am looking for information about its original distribution (is it native for N America?) as well as about its actual species range.

Thank you in advance for your comments and help.

Regards,

Radomir

Some species of Bangladeshi ECM fungi (bolete) are very close ancestor to Australian/Malaysian bolete in molecular analysis, some other saprophytic fungi as well. So, how they (ECM fungi or saprophytic fungi) distribute/migrate from Australia to South Asia or vice versa? What are the possible causes for the common disjunction between South Asian fungi and Australian fungi? 

Thanks for sharing your valuable idea.  

I am interested in whether or not there is any evidence of historical distributions of extant seabird groups in the North, particularly in relation to glacial recession, but have not been able to locate any specific sources for this information.

Im attempting to reconstruct precontact land-use in the Rockies around an archaeological site recently found along the Ram River. Beyond very few published sites, it seems to be hard to find information on sites in this area beyond consulting reports. I have information on the James Pass Site, Lake Minnewanka (Banff Area), Vermilion Lakes (Banff Area), The Patricia Lake Site (Jasper Area). Does anyone have reports from the Red Deer River Drainage? Or ongoing research in the Kootenai Plains? 

Thank you! 

We're producing SDMs for Central American birds from citizen science (eBird) data. Our models work really well (AUC typically around 0.95) when we don't include a bias grid, but when we add a bias grid (based on density of eBird observations), AUC falls significantly, and models predict species well outside their current range (from BirdLife database).

Surprised by this...anyone had similar experiences when using bias grids?

# observations (locations) range from 35 to high hundreds across our 28 species.

i have about 50 grids and have conducted honey's analysis using Devi Jankowitz rep grid manual. I further need better tools like clustering. 

i am working on distribution of a particular vulture species distribution in relation to climatic and anthropogenic factors only. So i am bit confuse whether it will be a ecology or biogeographical study or something else, as above mention topic are very vast and will it be appropriate to use any one of them?. Thank you

I'm searching for an English term (and possible some references) to define the introduction of an alien species in an area which belongs politically to the same Country of origin of the species but previously did not present for biogeography or ecological matters. For example this happened often with freshwater fishes. Thank you!

Is there any software, by which i can express site specific behavior of a particular captive animal( in enclouser)?

In Northern Europe, Chenopodium album, which is now recognized as a global weed species, was a secondary crop in Europe during the Iron Age. Although we have evidence that the species Chenopodium album L. had an importance as a crop in Europe, a domesticated form also existed in the Himalayas. Why researchers and breeders concentrated their efforts in Europe to adapt to temperate climates only the Chenopodium quinoa Willd, a tropical species. Considered for breeding programs this crop from the highlands of the Andes is adapted to growth at relatively low temperatures. The recent expansion of quinoa near the Mediterranean Sea is changing the context. Today, we could revise this view to use more adaptive capacities of C. album.

"Is there any possibility of bitumen/ asphalt releasing carbon dioxide while being heated upto 170 degree centigrade. Though its known that its ignition temperature is ~400°C still if you have any opinion or test results with you.... please share

It is well-known that different aspects on the same mountain may possess quite different enviromental traits or even species pools (e.g. in the northern hemisphere, the southern slope of a mountain is generally warmer and often drier than the northern slope of the same mountain). It is thus reasonable to infer that there may be different elevational patterns of species richness along different slope aspects on a mountain. However, such an effect seems to be ignored and most studies on elevational richness patterns generally survey one aspect on a given mountain. Could anyone recommend some related publications or does anyone have related studying experience in this field?

I'm curious if anyone has used the positive relationship between latitude and the length-dry mass power coefficients for aquatic insects found in this paper (https://www.researchgate.net/publication/259550032_The_biogeography_of_insects%27_length-dry_mass_relationships) and compared it with northern european populations?

Hi, 

I have two variables, Temp (T) and Latitude (L). I have a DEM (E). I need to interpolate T from point shape file to each pixel of E. 

the relation is as follow: 

T_E1,L1 = T_E0,L0 - (E1-E0)*G - (L1-L0)*P

where, T_E1,L1 = new interpolated raster value of each pixel

E0 = Elevation of temperature station 

E1 = Elevation of new location, which will be each pixel of raster DEM

L0 = latitude of station

L1 = latitude  of each pixel of DEM

G & P = constant values to multiply 

here, I am looking for R code or method to do this in ArcGIS. 

any clues are appreciated. 

many thanks. 

I wanted to know whether the universal primers like ITS, matK etc can help in resolving the members of a monotypic( single species) genus.

1. To use all species available for such mapping, even the correlated species ones, because they have slightly different distributions. Also, it seems to me that using all species available for such mapping will force a cluster in areas with the same species composition, and this is the objective of the mapping.

Or

2. Exclude the correlated species and use just one of them.

If someone has an opinion about that, I would appreciate.

If I want to conduct study about diversity and biogeography of coastal marine gastropod, is there any minimum area of sampling that required to obtain the information if i use plot method?