From d6c91ad4778adb163bcbbcd3ce6cf12fb5fc460e Mon Sep 17 00:00:00 2001 From: Neves-P
DAISIE FAQs
+Q1 – What is DAISIE?
+DAISIE (Dynamic Assembly of Islands through Speciation, Immigration +and Extinction) is a modelling framework implemented in an R package that +allows estimating rates of speciation (cladogenesis and anagenesis), +colonisation, extinction and a carrying-capacity for a focal assemblage +of island species based on phylogenetic information, for various +macroevolutionary models of island assembly. It also allows simulating +islands under rates for those processes. The method was first introduced +in Valente, Phillimore & +Etienne 2015.
+Q2 – What is DAISIEprep?
+DAISIEprep (Lambert et al +2023), is an R package that we have developed to help users prepare +the data for running DAISIE analyses. It is not compulsory to use +DAISIEprep, but it greatly helps! DAISIE and DAISIEprep are +two separate R packages that can be independently installed from CRAN. +DAISIEprep contains certain functions for extracting, plotting, and +visualising data that can be useful for those working on island +biogeography but who do not necessarily want to use DAISIE.
+Q3 – What input data do I need to have to run a DAISIE +model?
+DAISIE uses an unconventional data format. Since a DAISIE analysis is +centered on a focal island assemblage, it requires the times of +colonisation and speciation events for all the lineages that make up the +focal community. This information can come from various sources: a +single phylogeny for your group of interest if available, several +different phylogenies representing individual lineages that make up the +focal community, values obtained from the literature, or a mix of +sources. DAISIE can also handle some missing data (see below and Q14). +There is no way around it: DAISIE is very data demanding! But that is +why you can do very cool things with it 😊. DAISIE requires as input the +following data:
+Checklist of ALL native island species of your focal group +(e.g., a list of all amphibians on an island; all plants on an island; +all Orchidaceae species on an island; all passerine birds on an +island).
Island endemicity status for each of those species: +whether they are endemic to the island (occur only on the island) or +whether they are non-endemic (occur on the island and also +elsewhere)
Colonisation times for all the lineages of your focal +group that have colonised the island (these can be extracted from +phylogenies or from other estimates obtained from the +literature)
Speciation times (branching events) for all the lineages +that have speciated/radiated on the island (these can be extracted from +phylogenies or from other estimates obtained from the +literature)
Missing island lineages: island lineages of your focal +group for which phylogenetic data is not available. An island lineage is +a group of island species (one or more species) that descend from the +same mainland species. So, for example, an island radiation is a +lineage, but a single non-endemic species that has no close relatives on +the island is also its own island lineage. For example, if no +phylogenetic data is available for lineage x of your focal group, you +need to tell DAISIE that lineage x is present on the island and also how +many species belong to lineage x.
Missing island species: for island lineages for which +phylogenetic data is available for some of the species but not others, +you need to tell DAISIE the number of missing island species on the +lineage.
Island age: An estimate of the geological age of the +island (when did the island become available for colonisation, when did +the island first emerge).
Mainland pool size: An estimate of the size of the +mainland pool – how many species of the focal group occur on the +mainland (e.g., a list of all amphibians on the mainland; all plants on +an mainland; all Orchidaceae species on the mainland; all passerine +birds on the mainland) and could have colonised the island.
Q4 – What kind of questions can be addressed with +DAISIE?
+We answer this FAQ by providing examples of questions that have +already been addressed in different publications that have used +DAISIE.
+What are the rates of colonisation, speciation (cladogenesis and +anagenesis) and extinction for an island or archipelago? Examples: +Galápagos birds (Valente +et al 2015), Caribbean frogs (Jiménez-Ortega et al +2023), fishes of Lake Biwa Japan (Hauffe et al +2020).
How does island area, dynamic connectivity, geological history +affect phylogenetic and diversity patterns on islands? Examples: +Hawaiian islands (Neves +et al 2022), oceanic islands (Valente +et al 2014).
How old are island lineages under different (simulated) +scenarios? Examples: oceanic islands (Valente +et al 2014), continental, oceanic and land-bridge islands (Neves +et al 2022).
How does trait dependent diversification affect phylogenetic and +diversity patterns on islands? Example: Simulated data (Xie +et al 2023).
Is a radiation on an island exceptional? Examples: Darwin’s +finches (Valente +et al 2015), Caribbean frogs (Jiménez-Ortega et al +2023).
Do rates of colonisation, speciation and extinction differ +between different types of species (e.g. species that can fly vs those +that cannot)? Examples: bats and non-flying mammals of Madagascar (Michielsen et +al 2023).
Is a focal island assemblage at equilibrium? Examples: Galápagos +birds (Valente +et al 2015), Caribbean bats (Valente et al +2017a), birds of Macaronesia (Valente et al +2017). Is diversity on the island governed by ecological limits and +diversity dependence?
If diversity dependence is operating on the island, does it +operate at the level of the clade (within island lineages) or the island +(within and between island lineages)? Examples: Frogs of Caribbean (Etienne et al 2023), +Galápagos birds (Valente +et al 2015).
How long would an island take to recover diversity back to a +pre-human diversity under natural rates of colonisation, speciation and +extinction? Examples: birds of New Zealand (Valente et al +2019), bats of the West Indies (Valente et al +2017).
Do rates of colonisation, speciation and extinction vary through +time? Can we detect temporal shifts in rates? Examples: fishes of Lake +Biwa in Japan (Hauffe et al +2020).
If currently threatened species go extinct from an island, how +long would it take to return to today’s diversity under natural rates of +colonisation, speciation and extinction? Examples: birds of New Zealand +(Valente et al +2019), mammals of Madagascar (Michielsen et +al 2023).
How do speciation, extinction and colonisation rates vary with +island area and isolation on a global scale? Example: birds of oceanic +islands archipelagos worldwide (Valente et al +2020).
What do phylogenies of island taxa look like simulated under +different scenarios? Examples: continental, land-bridge and oceanic +islands (Neves +et al 2022).
Q5 - I have a time-calibrated phylogeny – +can I fit DAISIE to it?
+Yes, but not immediately. Unlike most other phylogenetic methods, +DAISIE does not use as input a phylogenetic tree (see Q1). In the +context of DAISIE, phylogenies are simply used to extract times of +colonisation and speciation and to identify island lineages resulting +from different colonisation events. Therefore, you can use a single +phylogeny or many different phylogenies to obtain this information. But +you can even run DAISIE without any phylogeny at all, provided you have +estimates for island colonisation and speciation times of your focal +species (but these are usually obtained from phylogenetic +information).
+Q6 – What does an ideal DAISIE dataset look +like?
+The ‘ideal’ DAISIE dataset would be an island community dataset with +colonisation and speciation times extracted from a time-calibrated +phylogenetic tree (e.g. Figure 1) with complete sampling, in which all +species of the focal group are included (preferably multiple individuals +of the same species) as well as all of their closest non-island +relatives. In practice this type of dataset is rare. For most insular +communities, there may be a few well-sampled phylogenies available for +some of the insular lineages, while other lineages may have poorly +sampled phylogenies, and for some lineages there may be no dated +phylogenetic data available at all. For some non-endemic species there +may be individuals from the mainland sampled in the phylogeny, but not +from the island. DAISIE can incorporate information from these +heterogeneous data types.
+Figure 1 – Visual representation of a typical dataset used +in DAISIE analyses. Modified from Lambert +et al 2023. In this hypothetical example, a focal island community +on the Hawaiian archipelago has nine species. Panel A shows the wider +global phylogeny in which the nine Hawaiian species are embedded +(highlighted). Panel B shows the separate phylogenies of those island +species from the perspective of the archipelago. Numbers on the plots +link the corresponding lineages from each panel. The island community +(B) consists of lineages resulting from four colonisation events, which +are spread out in different topological locations in the tree of the +taxonomic group at the global scale (A). Three of the island lineages +contain exclusively species that are endemic to the island and one +contains only a single non-endemic species. Two of the endemic lineages +have undergone cladogenetic speciation on the island, forming island +clades with more than one species. The colonisation time is assumed to +be the divergence time from the mainland sister species (stem age).
+Q7 – What should a focal island assemblage be in a DAISIE +analysis?
+The focal island assemblage (or focal community, or target group) can +be defined by the user, but it should make biogeographical and +ecological sense. It should be a group that can be defined by a common +source pool on the mainland. For example, if you work on plants, you may +choose to include all native species of plants, or focus just on a group +of interest, such as all ferns, all Asteraceae, all angiosperms. If you +work on birds, you may choose all bird species, but decide to exclude +migratory species as these do not follow classic colonisation “rules”. +What we do not recommend is cherry-picking lineages just because you +have phylogenies for them, and then excluding others for which you have +no phylogenetic data.
+Q8 - I have a large phylogeny (e.g. a plant family, or a bird +order) that includes many island species, can I run DAISIE?
+Yes, but please note that DAISIE is meant to be applied to a specific +island or archipelago. Just because your clade of interest has many +island species, it does not mean DAISIE will be a good match for it. For +example, if your group has 20 island species and each is found on a +different island, then it may be difficult to have a suitable dataset to +run DAISIE, because ideally you would need an island with multiple +colonisation events by your focal group. (Note: you could run such an +analysis if you assume that (most of) the rates of colonisation, +extinction and speciation are similar across islands. See this study on +Macaronesian birds).
+Q9 - I have a phylogeny of an island radiation, can I apply +DAISIE?
+An island radiation results from a single colonisation event of the +island so there is a single lineage. DAISIE is designed to estimate +colonisation, speciation and extinction rates for an island assemblage +composed of multiple independent colonist lineages, not for a single +island lineage. Therefore, we do not recommend applying DAISIE if your +focal group is a single radiation. If you are interested in a single +island lineage, there are more appropriate lineage-specific phylogenetic +methods than DAISIE, such as the diversity-dependent birth-death model +implemented in the DDD R package +(Etienne).
+Q10 - I have compiled phylogenies for several plant (or +animal) lineages from an island. Can I apply DAISIE?
+Yes, but you should not apply DAISIE to just a few groups and ignore +the other groups of your focal taxon that are present on the island. If +there are plant (or animal) lineages on the island that belong to your +focal group but for which phylogenetic data is not available, you need +to “inform” DAISIE about those missing lineages. DAISIE needs to know +how many lineages are missing from your focal group, and how many +species belong to each of those missing lineages.
+Q11 – Do I need to include non-endemic species, for example +widespread species found in multiple islands and +continents?
+Yes! DAISIE is meant to be applied to native island assemblages. +Therefore, both endemic and native non-endemic species are important! Do +not include just the island endemics in your analyses, because you would +be missing information on the natural colonisation events that gave rise +to the non-endemics. You might therefore underestimate colonisation +rates and overestimate anagenesis rates.
+Q12 – Should I include non-native species (introduced by +humans)?
+No. Species introduced by humans should normally not be included in +DAISIE analyses because they did not colonise under natural processes of +colonisation. *But note - if you wanted to consider only species +introduced by humans this could be possible, but this would constitute +an unusual type of analysis, because the rate of colonisation is +dependent on humans, not on the biogeography of the island.
+Q13 – Can I apply DAISIE to a subset of island lineages for +which I have phylogenies?
+DAISIE is designed to estimate rates for a complete island assemblage +(e.g. all amphibians on an island, all ferns on an archipelago). +Therefore, it is not meant to be applied to just a subset of those +lineages. So, for example, if you have an island that has 100 +colonisation events of your focal taxon (some have radiated, others have +not), it is not appropriate to just pick 40 for which phylogenetic data +is available and exclude the other 60 colonists and their descendants. +If you only have phylogenetic data for a subset of the island lineages +of your focal taxon, you can still run DAISIE, but you need to include +all the lineages for which no phylogenetic data is available as missing +lineages.
+Q14 – How much missing data is acceptable?
+This is a good question that we do not yet have the answer to. Of +course, the more complete the data, the better. So having colonisation +and speciation times for the majority of your island species and +lineages is preferred. But if you don’t have colonisation or speciation +times for many of the lineages, you can still include them in the +analyses by “informing” DAISIE that you know that they are present on +the island but you just don’t know their colonisation or speciation +times. This information is useful for DAISIE. We wouldn’t recommend +doing this for all lineages and species because then DAISIE only knows +that the species are there, but doesn’t have any temporal information to +make inferences on. So in sum: the more phylogenetic data (colonisation +and branching times) the better, but having many missing species or +missing lineages is also fine!
+Q15 - How to handle island species that are not monophyletic +on the phylogeny?
+For example, what to do when two island individuals of (presumably) +the same species are retrieved in different positions in a phylogeny? In +these cases the user should make a decision based on their knowledge of +the taxa and system. If the user thinks that the non-monophyly may +indicate that the taxon should be split into different species, then +they may consider increasing the number of species in the island +lineage, and, if appropriate, increasing the number of island +colonisations (e.g. there may be cases where the same species colonised +the island multiple times). If the user thinks the non-monophyly is due +to incomplete lineage sorting or due to a mis-identification, then the +user may consider revising the phylogeny, or choosing a node to infer +the lineage age that reflects uncertainty (e.g. picking an older node +and using this as maximum time of colonisation).
+Q16 – How to define the number of species in the mainland +pool?
+The number of species in the mainland pool should be the number of +species on the mainland that belong to your focal group that could have +colonised the island since the island became available for colonisation. +The mainland itself can be defined by the user depending on the location +and isolation of the system (e.g. a nearby larger island, a continent). +From our experience, varying the mainland pool affects the colonisation +rate estimated in DAISIE, but does not alter other parameters or affect +model selection (in general). If you are unsure about which mainland +pool size to use, you may consider running sensitivity analyses using +different mainland pool sizes, to see how that affects the results.
+Q17 – How to obtain data on island age?
+Island age estimates can be obtained from the biogeographical or +geological literature (e.g. see the Methods section of Valente et al +2020 for the sources of the island ages used there).
+Q18 – Can I use DAISIE without DAISIEprep?
+Yes, you can prepare your DAISIE dataset “by eye” without using +DAISIEprep. But DAISIEprep will be very useful if you have large +datasets and it also greatly helps with reproducibility (and avoids +trying to find clades in a phylogeny by eye, instead doing it +automatically).
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