Information

What do you call clearly different sub-groups within a species?


If you look at species of bees and ants, you can clearly see there are drastically different specialized ants, like queen ants and workers. They're both part of the same species, yet are still obviously different. What is the proper name for that phenomena?


In eusocial insects, especially ants and bees, these groups are called "castes" (see e.g. Hölldobler & Wilson, 1990. This is the same term that is used for social stratifications in some human societies e.g. in India.

One definition of caste is:

… the physical or the behavioural/physiological phenotype of a eusocial individual, or both.

(from Hölldobler & Wilson, see also antwiki.org)

Some division of labour as well as collective rearing of young can occur in prosocial animals as well, but there the term caste is not used.


Unsorted Homology within Locus and Species Trees

Diego Mallo, Leonardo De Oliveira Martins, David Posada, Unsorted Homology within Locus and Species Trees, Systematic Biology, Volume 63, Issue 6, November 2014, Pages 988–992, https://doi.org/10.1093/sysbio/syu050

The concept of homology lies at the root of evolutionary biology. Since the seminal work of Fitch (1970), three main categories of homology relationships have been defined at the molecular level: orthology, paralogy, and xenology. In brief, if two gene copies arose by duplication they are paralogs, whereas if they arose through speciation they are orthologs. If one of them was transferred from a contemporaneous species, we call them xenologs (Supplementary Fig. S1 in Supplementary Material online, available at http://dx.doi.org/10.5061/dryad.87k57 see Gray and Fitch (1983) Fitch (2000)). Indeed, these terms were coined under a phylogenetic framework in which species were represented by single individuals, and as such they have remained very much intact during the last four decades—although particular cases within these categories have received specific names ( Mindell and Meyer 2001). However, advances in sequencing technology have changed the field, and it is now very common to collect data sets containing multiple gene loci and/or multiple individuals per species. In general, such genome-wide data sets not only have unveiled extensive phylogenomic incongruence ( Jeffroy et al. 2006 Salichos and Rokas 2013) but have brought back to the spotlight the consideration of how ancestral polymorphisms sort within populations ( Edwards 2009). Altogether, phylogenomic data make imperative the explicit distinction between organismal and gene histories.

Let us consider phylogenetic relationships at three different levels: species, loci, and gene copies ( Fig. 1). The distinction between species/population trees and gene trees has been known for decades ( Goodman et al. 1979 Pamilo and Nei 1988 Takahata 1989), whereas the introduction of locus trees into these models is very recent ( Rasmussen and Kellis 2012). In brief, a species tree depicts the evolutionary history of the sampled organisms. In this case, the nodes represent speciation events, connected by branches that reflect the population history along these periods, and where their widths represent effective population size ( ⁠ N e ⁠ ) and their lengths represent time (usually in years or number of generations). Apart from speciations, only evolutionary processes that affect species as a whole are represented at this level, like hybridization. Note that species trees are equivalent to population trees when the organismal units of interest are conspecific populations. In this case, the nodes of the population trees represent isolation events. In general, we will refer to “species” as any diverging, interbreeding group of individuals regardless of its taxonomic rank. On the other hand, a locus tree represents the evolutionary history of the sampled loci for a given gene family (see Rasmussen and Kellis 2012). Since the loci exist inside individuals evolving as part of a population, the locus tree is embedded within the species tree. In a locus tree, the nodes depict either genetic divergence due to speciation in the embedding species tree or locus-level events such as duplication, losses, or horizontal gene transfers, whereas the branch lengths and widths represent time and N e ⁠ , respectively. Here, we assume that the locus-level events get immediately fixed in the population, so these N e are equivalent to those in the species tree and are the same for every locus. Finally, a gene tree represents the evolutionary history of the sampled gene copies that evolve inside the locus tree. Gene tree nodes indicate coalescent events, which looking forward in time correspond to the process of DNA replication and divergence, and that can occur around the speciation time, well before (deep coalescence) or afterwards (migration in population trees). The branches of the gene tree usually represent amount of substitutions per site, and can also represent number of generations or other measures of time.

Species, locus, and gene trees. The figure represents the phylogenetic relationships between three gene copies (A0, B0, and C0) (gene tree = thin dark lines) belonging to a single locus (locus tree = medium-thick lines) in three different species (A, B, and C) (species tree = thick light tree in the background). Internal gene tree nodes (i.e., coalescences) are numbered and represented by black circles. The terminal gene tree nodes represent single gene copies. In this case, the species, locus, and gene trees are fully concordant.

Species, locus, and gene trees. The figure represents the phylogenetic relationships between three gene copies (A0, B0, and C0) (gene tree = thin dark lines) belonging to a single locus (locus tree = medium-thick lines) in three different species (A, B, and C) (species tree = thick light tree in the background). Internal gene tree nodes (i.e., coalescences) are numbered and represented by black circles. The terminal gene tree nodes represent single gene copies. In this case, the species, locus, and gene trees are fully concordant.

Importantly, these three historical layers do not necessarily coincide. True species/population trees can differ from true locus trees due to gene duplications, losses, and/or horizontal gene transfers, whereas true gene trees can differ from their embedding locus and species trees if there is incomplete lineage sorting (ILS) ( Maddison 1997 Page and Charleston 1997) (and migration in the case of population trees). In this regard, Avise and Robinson (2008) defined “hemiplasy” as the topological discordance between gene trees and species induced by ILS, resulting in apparent homoplasies. However, the problem is that the standard homology subtype definitions do not explicitly consider this potential disagreement because they were coined in reference to a labeled (with loci and species names) gene tree. However, to fully take into account the complexity of the evolutionary process, we find it crucial to understand that homology relationships depend on the interaction of these three layers. This is essential not only from a conceptual point of view, as we will show below, but also for practical evolutionary inference. In our opinion, the decoupling between species trees, locus trees, and gene trees, and the concomitant multilineage considerations imply a revision of the classical homology relationships. Here, we introduce new terms to describe homology scenarios in which orthology and paralogy are not clearly distinct due to lineage sorting. For the sake of argumentation we will adopt a neutral, multispecies coalescent model with gene duplication, loss, and transfer (see Rannala and Yang 2003 Rasmussen and Kellis 2012). This implies free recombination between loci but no recombination within them, and no gene flow following speciation or population subdivision. For didactic purposes, we will only discuss simplified scenarios were (i) there is one allele per locus, (ii) new loci can be gained but never lost, and (iii) there is no duplication polymorphism (i.e., every individual in a species has the same loci). Importantly, our propositions would hold under more complex scenarios, but these would unnecessarily complicate the explanation.


Observing Variation

By learning the skill of scientific sketching, students will learn to better observe and document the natural world. This simple-to-lead activity gets them closer to constructing explanations for the variation of traits seen within a species.

At the end of this lesson students will be able to:

  1. identify patterns of similarities and differences in traits shared between specimens.
  2. create a scientific sketch that communicates information that can be used by other scientists.
  3. construct an explanation for how an individuals’ variation might effect the survival of a larger population.
  • specimens from same species (1 per student)
  • student field journal (1 per student)
  • pencils
  • make copies of the student field journal (1 per student)
  • gather several specimens of the same species (1 per student)

Teacher Tip: You can choose whatever type of specimen that you like, but they should all come from the same species. We’ve used a variety of types of specimens from leaves to peanuts to oranges to sea shells. Make sure that whatever specimens you are collecting for this activity, have been collected in a sustainable manner.

If your students have already learned about genetics, take a moment to review that DNA is the genetic material found in the chromosomes of cells. Review that DNA is a molecule composed of genes and that mutations are genetic changes that result in increased variation within a species.

If your students are new to heredity, ask them whether they think all individuals of the same species look the same. Then ask, why they think there is variation within species.

Tell students that in this activity they will use scientific observation skills to observe a range of natural variation within a single species, and then think about what environmental factors might influence the survival of specific variations over another.

  1. Select as many specimens of the same species as there are students and place them in a central location.
  2. Explain that these are specimens of a single species.
  3. Let all students examine all specimens. Ask them to look for variation.
  4. Ask each student to select a specimen.
  5. Pass out the student field journals and tell students to sketch their specimen. Encourage students to measure the specimen and add any descriptive notes that will help them identify their specimen.
  6. When they have finished the field journal, have small groups (5 to 8 students) mix their specimens up and try to find them again based on their sketches.
  7. Have students reflect on what parts of the sketch helped them identify their specimen. Then, give them a chance to add a few more details to their sketch.
  8. Mix the specimens back together again, and have students switch sketches with a classmate. Can someone who didn’t observe the same specimen identify it based on the sketch and notes of the first student?
    • Teacher Tip: This emphasizes the importance of acute observation and detailed documentation, especially when other scientists will be using your work.
  9. Have students reflect on what they think a good scientific journal entry would entail. Ask questions such as: What observations were particularly useful in finding your specimen or your classmate’s specimen? What other details, words or measurements could have made it easier to find the correct specimen? How does sketching vs. taking a picture help you notice the details of a specimen?
  1. Have students read about a specific example of species variation that scientists have studied: www.mothscount.org/text/63/peppered_moth_and_natural_selection.html
  2. Ask students to use the 2 nd side of their field journal to think about how the variations they observed in their specimens might be beneficial or detrimental for an individual.
  3. Then, discuss and reflect upon the following questions.
    • What types of variations did we see in the specimens? (Color, size, shape, number of spots, etc.)
    • How do you think variation in these species comes to be? (Variation arises through different combinations of genes inherited from the parents and through the continual mutation of genes. Some variation among individuals is not genetic, but is due to specific events or environmental influences during an organism’s life.)
    • Why is variation important in populations? (Variation increases the likelihood that at least some individuals will survive to reproduce no matter how environmental conditions change. Variation is also a key step in the evolutionary process. It is a prerequisite for evolution to occur.)
    • Can you see all genetic variation? (No. A lot of genetic variation is hidden from the eye.)

“Variation fuels the process of evolution. No two individuals of any species are exactly alike. Even if they look similar, differences in their genes distinguish one from the other. While subtle, those differences may allow some to live longer and produce more offspring than others. That process – called natural selection – drives evolution.” – California Academy of Sciences exhibit text.

Variation is a fundamental prerequisite in order for evolution to occur. To see natural variation, all you have to do is look around you. Human beings, as with all species, exhibit a range of natural variation that is visible. We have different shaped faces, different eye colors, different skin colors, and much more. We also have variations that are not visible in our appearance, yet they are observable, such as human blood type.

These natural variations within a single species arise for a variety of reasons. One major reason that organisms who reproduce sexually have variation is because each individual has a different combination of genes inherited from their parents. But, there is still some variation in variation as is clearly evident in siblings who have the same parents but inherit different genes making them genetically different from one another.

In addition to genetic variation resulting from parents, other causes of genetic variation include the movement of genes from one population to another (gene flow), and changes in the DNA (mutations), which are constantly arising within natural populations.

Furthermore, variation can be a result of different environmental factors. For example, an animal that has access to larger prey may grow larger, while an animal that has only access to smaller prey may not grow as big.

In this activity - Observing Variation – students will observe variation within a single species. Practicing observation is an important scientific skill. After all, Darwin’s observation of variation within and between species was the initial step in his development of the theory of evolution by natural selection.


1 INTRODUCTION

During the last 15 years, following the success of the DNA-barcoding projects and the increase in sequencing capacities, many methods of species delimitation based on DNA sequences have been developed. They can be approximately classified into two main categories. The first category includes methods that compute the likelihood of competing partitions of species hypotheses (“models”) in the so-called “multispecies coalescent” framework. In this category, the most popular methods are SpedeSTEM (Ence & Carstens, 2011 ), BPP (Yang & Rannala, 2014 ) and BFD (Leaché et al., 2014 ), reviewed (with other methods) in several articles (Camargo & Sites, 2013 Carstens et al., 2013 Fujita et al., 2012 Leavitt et al., 2015 Rannala, 2015 ). They were designed for multilocus data and are computationally (extremely) demanding. As a consequence, they have been mainly applied to data sets with limited number of sequences and species, and to well-studied groups, for which competing partitions of species have been proposed in the literature they generally correspond to species complexes, typically in the grey zone (De Queiroz, 2005 ).

A second category of methods corresponds to exploratory ones, i.e., methods that propose de novo species partitions, typically from a single-locus, DNA-barcoding-like, data sets. Although sometimes criticized because a single gene tree poorly represents the species tree (Degnan & Rosenberg, 2009 Nichols, 2001 ), these methods are widely used, as they are easy to apply on DNA-barcoding data sets, even large, and precisely because they do not necessitate predefined species hypotheses. The most popular are general mixed Yule-Coalescent model (GMYC) (Pons et al., 2006 ), Poisson tree process (PTP) (Zhang et al., 2013 ), both first developed in a maximum likelihood framework, and later extended to a Bayesian framework (Reid & Carstens, 2012 ), and automatic barcode gap discovery (ABGD) (Puillandre et al., 2012 ). GMYC and PTP take a phylogenetic tree as input and estimate rates of branching events to infer which part of the tree more likely follows a speciation model (the deepest part) and which part follows a coalescent model (subtrees of the shallowest part). The species partition is found by maximizing the likelihood of the transition between these two branching rates, GMYC in absolute time (hence the need for an ultrametric tree), PTP in mutational time at different nodes of the tree. GMYC first inferred a single transition event between the two rates (speciation versus coalescent) PTP first had two rates (speciation and coalescent). Both were later expanded to infer “multiple thresholds”, allowing several transitions to occur in different subtrees (Kapli et al., 2017 Monaghan et al., 2009 ).

Contrary to the two previous methods, ABGD uses only pairwise genetic distances (no tree is inferred) and automatically identifies in their distribution the so-called “barcode gap”. This gap marks the limit between the smaller intraspecific distances and the larger interspecific distances. From the gap, a distance threshold is estimated and used to partition the samples into putative species. A coalescent model is used to identify the position of the most likely barcode gap, based on a maximal genetic intraspecific divergence P defined a priori by the user. Consequently, users must provide a range of P in which ABGD identifies one or several barcode gaps and the method outputs the corresponding species partitions. For a single data set, ABGD thus eventually proposes several partitions that correspond to different prior values P. In its recursive version, ABGD is applied on each group of the initial partition, and eventually splits them when internal barcode gaps are detected.

The relative performances of these three exploratory methods, GMYC, PTP and ABGD, sometimes together with less used methods (Flot et al., 2010 Ratnasingham & Hebert, 2013 ) have been compared in various taxa: mammals (Derouiche et al., 2017 ), amphibians (Vacher et al., 2017 ), squamates (Blair & Bryson, 2017 ), fishes (Ramirez et al., 2017 ), echinoderms (Boissin et al., 2017 ), insects (Lin et al., 2015 ), spiders (Ortiz & Francke, 2016 ), crustaceans (Larson et al., 2016 ), pycnogonids (Dömel et al., 2017 ), rotifers (Papakostas et al., 2016 ), annelids (Decaëns et al., 2016 ), molluscs (Fourdrilis et al., 2016 ), flatworms (Scarpa et al., 2017 ), nemerts (Leasi & Norenburg, 2014 ), cnidarians (Arrigoni et al., 2016 ), plants (Lithanatudom et al., 2017 ), algae (Zou et al., 2016 ), lichens (Pino-Bodas et al., 2018 ), fungi (Alors et al., 2016 ) and foraminifera (André et al., 2014 ).

Although the results obtained with the various methods often vary depending on data set characteristics (e.g., Blair & Bryson, 2017 ), the main conclusions of these studies are: (a) All methods generally perform well (but see e.g., Dellicour & Flot, 2018 ) being mostly congruent (i.e., providing similar species partitions) with each other and with the species partitions inferred from independent data (e.g., other molecular markers, morphological data, ecological data) (b) All of them perform poorly when the number of sampled individuals per species is too low (Ahrens et al., 2016 ), or when the contrast of intra- versus interspecific divergences is mild. This contrast varies with species ages, mutation rates, population sizes, strengths of the selection and degrees of within-species population structure (Pante et al., 2015 Pentinsaari et al., 2017 Ritchie et al., 2016 ) mPTP was in particular developed to overcome this issue (Kapli et al., 2017 ) (c) Partitions proposed by the three methods sometimes differ, each of them being able to infer the “correct” species when the two others fail. This led some authors to propose that all three methods (among with eventually others) should be applied jointly and compared (Ducasse et al., 2020 ) and (d) Although there are several exceptions (e.g., Blair & Bryson, 2017 ), ABGD in particular, and PTP to a lesser extent, tend to lump species more than GMYC (Pentinsaari et al., 2017 ). Conversely, the multiple-threshold version of GMYC is particularly prone to oversplitting (Fujisawa & Barraclough, 2013 Kekkonen & Hebert, 2014 ).

In comparison with GMYC and PTP, ABGD has the advantage of being very fast, mainly because it bypasses the phylogenetic reconstruction. Furthermore, because ABGD identifies a species partition for each value of P defined a priori, several partitions may be proposed, reflecting the uncertainty stemming from the data and encouraging the user to evaluate the relevance of the ABGD partitions in the light of other data, as it is recommended in an “integrative taxonomy” approach. However, ABGD does not provide a score for each partition that would help the user to identify the “best” partition(s), and this probably constitutes the main drawback of ABGD (judging from the numerous comments and questions the authors of ABGD have received from the users).

In this article, we describe a new method of species delimitation, still based on pairwise genetic distances, but which implementation provides a score for each defined partition and overcomes the challenge of a priori defining P. Our new algorithm, ASAP, still provides several partitions, more or less fine-grained, but ranked using a new scoring system. Importantly, we also develop a full graphical web-interface to ease its usage. However, ASAP, like any other method, must not replace the taxonomist work, as any partition of species must be subsequently tested against other evidences in an integrative taxonomy framework. This is especially crucial as ASAP uses single-locus data that are known to bear weaknesses.


Discussion

High Caenorhabditisspecies richness in a tropical rainforest

Here we documented the extensive sampling of Caenorhabditis in a tropical rainforest in French Guiana and characterized the structure of genetic diversity of the cosmopolitan species C. briggsae from small (

1 km) and up to global spatial scales. We identified six species from a single tropical site, representing nearly 25% of the 26 Caenorhabditis species known in laboratory culture [3]. Three of these species may be endemic to this region, although sampling of Caenorhabditis in South America is very limited. These findings reinforce the view that Caenorhabditis nematodes can be locally diverse and – although they have been generally referred to as soil nematodes – are more easily found in rotting vegetal matter, especially fruits, flowers and stems [3, 13].

Our sampling can be contrasted with a recent extensive sampling effort in temperate France [13]. In mainland France, just two species of Caenorhabditis are found commonly: C. elegans and C. briggsae. In addition, C. remanei and C. sp. 13 each have been isolated once in the course of sampling many locations in France over many years [13]. The isolation of six distinct Caenorhabditis species in just a few square kilometres of tropical forest, including three potentially endemic species, testifies to much higher species richness of Caenorhabditis in the tropics [3]. Moreover, this finding for Caenorhabditis is fully consistent with latitudinal diversity patterns documented for many other taxa [25, 26]. As discovery of new species in this group is progressing rapidly, phylogenetically-informed analysis of Caenorhabditis species distributions may shed light on long-standing questions about the causes of latitudinal species diversity gradients [27].

Previous sporadic sampling of Caenorhabditis nematodes in Tropical South and Central America has yielded C. sp. 11, C. brenneri, and C. briggsae. An additional three species have also been found on Caribbean islands (C. sp. 14, C. sp. 19, and C. sp. 20) [3]. The absence of the well-known C. elegans in the Nouragues Natural Reserve is not surprising, however, given that this species is rare in previous sampling from the tropics [3]. Thus, the distribution of Caenorhabditis species around the world is consistent with there being a few cosmopolitan species and many other species endemic to particular geographic regions.

Our study demonstrates the first evidence of heterogeneous species distributions of Caenorhabditis at an intermediate spatial scale on the order of kilometres. It will be important in future work to determine whether these species distributions reflect stable features that might correspond to distinct ecological habitat characteristics of the different species, or instead reflect stochastic local abundances that are dynamic in time, perhaps owing to strong metapopulation dynamics associated with ephemeral food patches that can be utilized by many Caenorhabditis species. Co-occurrence of multiple species was common for samples of the same substrate type, and sometimes within the same sample, a pattern also reported for the less species-rich sampling in mainland France [13]. These observations raise the neglected issue of niche space in Caenorhabditis biology as a major question to be answered to understand the abundance and distribution of species. Unfortunately, there are few data describing Caenorhabditis fitness reaction norms in relation to potential ecological factors that could differentially limit species persistence (e.g. temperature, bacterial food specificity, substrate chemistry) [13, 22, 28–30].

Spatial structure of genetic diversity

We used the cosmopolitan C. briggsae as a focal taxon for quantifying population genetic variability from the finest sampling scales within the Nouragues forest samples up to pooled samples at regional and global scales. We found that distinct C. briggsae genotypes co-exist at scales down to a few metres (Montagne des Singes) or even a single fruit (Nouragues, sample H6). Given their highly selfing mode of reproduction in nature [6, 13], this suggests that a given fruit can be colonized by multiple individuals of distinct genetic backgrounds. These results mirror findings for temperate latitude samples of C. elegans, in that high local diversity may occur while genetic differentiation among locations is low [8, 10, 11, 14, 31, 32]. This pattern of large-scale homogeneity coupled with fine-scale heterogeneity also is reminiscent of the 'chaotic genetic patchiness' observed for some intertidal invertebrates with a highly dispersing planktonic stage [33]. In contrast to C. elegans, however, strong population structure dominates the global scale in C. briggsae, with 1) a large "Tropical/I" phylogeographic group distributed widely in the tropics around the world, 2) a large "Temperate/II" phylogeographic group having very low polymorphism overall and hence undetectable local diversity, and 3) a few genetically divergent clades, so far each found only in one place (Nairobi, Kenya Montreal, Canada Tai-an, Taiwan Hubei, China Kerala, India) [16, 19]. It is likely that such geographically restricted diversity is not yet exhausted by our sampling, nor are the possibilities for observing recombination among the main phylogeographic groups. Recombination had been previously noted at this large scale [6, 20] and can also be inferred among the French Guiana multilocus genotypes, as visualized by the reticulation pattern of the haplotype network (Figure 5B).


Discussion

We sampled a medium number of male and female individuals (median 20 total) of 136 arthropods species for Wolbachia, a reproductive parasite well known to be common in various arthropod taxa [9, 10], for Cardinium, a reproductive parasite known to exist widely but in fewer species [11, 12, 22], and for five other unrelated reproductive parasites whose incidence and prevalence were largely unknown. The observed incidence of infection for arthropods was 32.4% for inherited bacteria putatively acting as reproductive parasites.

Our results reveal that Wolbachia is, as expected, the most common reproductive parasite clade associated with arthropods, being recorded in 22.8% of species in our sample. Three other clades, Cardinium, S. ixodetis and Arsenophonus bacteria were present widely, with each occurring in 4% to 7% of the arthropod species. Whilst there has been some work on the former of these bacteria, S. ixodetis and Arsenophonus clearly represent 'understudied groups' that merit careful investigation. We would also note that the frequency of these four bacteria means that around one fifth of infections co-occurred with other species of inherited bacteria (8 of 44 infected species carry two different bacteria), an estimate of course made conservative by our own restrictive sampling for 'known' symbiont groups. This observation reinforces the call of Weeks et al. [37] to adequately sample the inherited flora of a species before interpreting data in terms of particular inherited bacteria.

There were three clades of bacteria that were either found in just one species or not found: Rickettsia, S. poulsonii and flavobacteria relatives. With respect to flavobacteria, the PCR assay detected allied clades of beneficial bacteria and was thus broad spectrum. We can thus be clear that this bacterial clade does not commonly reach mid or high prevalence outside ladybird beetles, where infection was initially established [38]. It is possible that this bacterial group is phylogenetically restricted to being 'ladybird MK'. The low incidence of Rickettsia was more surprising. These have been conjectured as being common, understudied bacterial symbionts of arthropods [39], but we can be confident that spotted fever group Rickettsia does not commonly exist at medium to high prevalence. This comment is made with the caveat that our screen for Rickettsia was relatively narrow, designed to find bacteria allied to a clade of ladybird MK, and would exclude some Rickettsia. Finally, there is S. poulsonii, otherwise known as group I spiroplasmas [40]. Other spiroplasmas were detected in the assay, indicating the PCR assay had a relatively broad catch. S. poulsonii itself is a MK associate of Drosophila species [41], with related strains in leafhoppers. Clearly, whilst spiroplasmas may be common, this particular clade either has low incidence, or always has low prevalence (as is the case for S. poulsonii in Drosophila, for example [42]).

As there is an intuitive link between the frequency of symbiotic infection and the overall importance of symbionts in arthropod biology, some comment on the true incidence level of these bacteria is appropriate. Given that we have tested against the presence of false positives in the PCR assay by obtaining product sequence in all cases, we would emphasise that our estimate underscores true incidence. Two main sources of underestimation of incidence are inherent in our survey. First, there is the possibility of false negatives in the PCR assay. These would be individuals (and, hence, species) in our sample that are in fact infected, but where infection has not been detected. Second, there are species where the PCR assay was accurate and our samples were truly uninfected, but other members of the species, not sampled and tested, are in fact infected. We would argue that both of these factors lead to a considerable underestimation of the frequency of infection.

False negatives with respect to undetected presence in infected samples are an issue with PCR assays, their sensitivity to titre and their ability to detect diverse infections. For Wolbachia, for instance, our use of a PCR assay based on 16S rDNA is likely to include most of the Wolbachia diversity. For Rickettsia, we would note that whereas we found no Rickettsia infection among spiders, Goodacre et al. [24] used PCR primers with a broader 'catch' and reported 19.7% of species to be infected by Rickettsia strains related only distantly to Rickettsia MK strains. These are likely to be inherited bacteria, and possibly reproductive parasites, but they would not be detected in our screen. Furthermore, we probably also underestimated the number of bacterial strains present in species we found to be infected. Given that our survey is in most cases based on PCR amplification of fragments of the slow evolving 16S rDNA sequence, we had limited power to detect multiple infections of closely related bacterial strains. For instance, the 16S rDNA sequences of Wolbachia infecting the mosquito Culex pipiens are well known to be strictly identical, suggesting that only one Wolbachia strain could occur, but sequencing of faster evolving genes has demonstrated the occurrence of more than 60 Wolbachia strains in this host species [43–45].

The second issue that causes an underestimation of the frequency of these agents is failing to sample an infected individual in an infected species. There are two aspects to this, the first being cases where infections are rare within a population. For example, MK infections tend to exist at low prevalence and examples of infection at between 1% and 10% frequency in females represent about one-half of all known infections [46]. Within our survey, we sampled two species in which just 1 of 20 individuals was infected, which clearly indicates the potential for false negatives arising from low prevalence infection. The second cause of failure to sample an infected individual arises from infection presence varying from population to population. We sampled seven species from several localities and revealed three examples of the presence or absence variation between populations within Western Europe. Such geographical variation is not uncommon [47], and is likely to be much greater when the scale of sampling is increased beyond Western Europe (which because of the recent ice age represents one recently recolonised region in ecological terms). Insufficient geographical sampling will lead to serious underestimation of infection incidence.

Overall, therefore, our point estimate of 32.4% of species infected with bacteria allied to reproductive parasites is likely to seriously underestimate the true figure. Our data improve on past surveys by increasing the intensity of sampling within species. For instance, for the case of Wolbachia, resampling our data (taking one individual from each species that is infected with a probability of infection given by the overall prevalence found) indicates that the move from single individual sampling to our modest multiple individual sampling reveals around one-third more cases of infection: the median Wolbachia incidence on sampling one individual per species is 17.6%, rather than the observed 22.8%. However, the sample size within each species is still limited and, most importantly, the restriction in geographical sampling may produce a very serious underestimation of symbiont presence or absence.

We obtained some insight into the degree to which host taxa vary in the frequency of their interaction with inherited bacteria. The depth of conclusion is very limited by virtue of the intensity of sampling within particular clades in a broad survey. Nevertheless, spiders (the Araneae) harboured a higher richness of inherited bacteria than others and represented diversity hotspots for these bacteria with 61.5% of species infected, contrasting to the relatively low incidence observed within Diptera and Coleoptera. The Araneae hotspot was present for Wolbachia, Cardinium and S. ixodetis, although not for Arsenophonus. Why some arthropod taxa are hotspots for inherited bacteria remains one of the most challenging questions with regard to the ecology of reproductive parasites. Certain taxa are clearly more susceptible to acquiring bacteria via horizontal transfer and/or to stably maintaining infection. Given that cocladogenesis is rare, it is the establishment of new infections that appears important in dictating incidence [48]. Intimate contact with other species is likely to predispose to transfer, be this parasitism, predation, physical damage or becoming prey [49–53]. Indeed, species which include other living arthropods in their diet through predation or parasitism are more frequently infected (43.8%) than other species (26.1% P = 0.05, Fisher's exact test). As a result, predation and/or parasitism could be an efficient transfer mechanism to elucidate the origin of hotspots, as illustrated by Araneae, which is exceptional because all species of this group depend completely on predation of other invertebrates which are largely polyphagous [54].

An alternative hypothesis to account for heterogeneity of endosymbiont incidence among host clades is based on differences in host phylogenies [55], but this does not seem to be a likely explanation for the Araneae.


Revisions in the Linnaean Classification

Linnaeus published his classification system in the 1700s. Since then, many new species have been discovered. Scientists can also now classify organisms on the basis of their biochemical and genetic similarities and differences, and not just their outward morphology. These changes have led to revisions in the original Linnaean system of classification.

Figure 2.4.3 The three domains of life and major groups within.

A major change to the Linnaean system is the addition of a new taxon called the domain. The domain is a taxon that is larger and more inclusive than the kingdom, as shown in the figure above. Most biologists agree that there are three domains of life on Earth: Bacteria, Archaea, and Eukarya . Both the Bacteria and the Archaea domains consist of single-celled organisms that lack a nucleus . This means that their genetic material is not enclosed within a membrane inside the cell. The Eukarya domain, in contrast, consists of all organisms whose cells do have a nucleus, so that their genetic material is enclosed within a membrane inside the cell. The Eukarya domain is made up of both single-celled and multicellular organisms. This domain includes several kingdoms, including the animal, plant, fungus, and protist kingdoms.

The three domains of life, as well as how they are related to each other and to a common ancestor. There are several theories about how the three domains are related and which arose first, or from another.


Why Humans Feel a Need to Belong: Beware of Animal Analogies

When things seem simple, research shows they're not

"The need to belong, also often referred to as belongingness, refers to a human emotional need to affiliate with and be accepted by members of a group." —Kendra Cherry, "How the Need to Belong Influences Human Behavior and Motivation"

An essay called "The Biology of Belonging" contains very useful information about how oxytocin, cortisol, and mammalian brains work to influence various patterns of social behavior however, sweeping generalizations about the ways in which sociality—social organization and social dynamics—has supposedly evolved and unfolds during the lives of nonhuman animals (animals) contain many factual errors. I received a few emails about this and simply want to set the record straight because things aren't quite as linear as they're portrayed and what we're told makes it seem like the evolutionary and current stories about within and between-group (herds, packs, and other aggregations) patterns of social behavior are simple when research shows they're not.

I also was motivated to write this brief piece based on what Eleanor wrote to me: "What do you think of the examples of animal behavior in this paper? I have lots of ideas about what makes humans tick but don't have the expertise to write about them and never would. If you have the time, can you kindly say something?" We can learn many life lessons from other animals, but it's essential to get things right. Animal behavior isn't all that straightforward, and that's what makes it so exciting to study. To this end, I offer a good number of references, most of which are easy reads and available online.

Variability, flexibility, and adaptability are the spice of life for numerous animals

Research in ethology and behavioral ecology has clearly shown that very few sweeping explanations really work to portray accurately why group-living individuals do what they do in different contexts. In fact, one of the joys of studying animals both in captivity and in the field is that there is a good deal of variability within (intraspecific) and between (interspecific) species as ecological and social contexts change over time.

I've had the great fortune of studying the social behavior of a number of different and diverse animals, both in captivity but mainly in the field (coyotes, domestic dogs, and various birds, including Adélie penguins in Antarctica), and just when my research assistants, colleagues, and I thought we had it all figured out—why individuals and groups were doing what they did and came up with sweeping answers—we rapidly learned we only had a fairly good or poor handle on what they were doing in those moments and marveled about the amount of variability in behavior we observed over time, sometimes during very short periods of time.

Of course, the variability we observed showed clearly that individuals and often groups were using different combinations of behavioral, cognitive, and emotional cues, often mediated by oxytocin, cortisol, and other chemicals, to change their behavior if and when ecological and social contexts changed. So, for example, claiming something like, "Coyotes live in packs" or "Coyotes live in pairs or on their own" ignores that these amazing and incredibly adaptable mammals display all sorts of social patterns depending on available food, who's around, and what they're doing and how they're feeling. 1

The same is true—within and between species variability—for just about all of the mammals and birds with whom I'm familiar and about whom I've read in textbooks, books dedicated to specific taxa and behavior patterns, and in research and other papers. 2 Other vertebrates, including fishes, reptiles, and amphibians, and some invertebrates also display variability in behavior as circumstances—social and nonsocial—change. 3,4

Spiders are amazing animals. Consider jumping spiders who routinely adapt to changing conditions. These amazing spiders, of which there are more than 6,000 described species, are "distinctive for development of behavioral flexibility, including conditional predatory strategies, the use of trial-and-error to solve predatory problems, and the undertaking of detours to reach prey. Predatory behavior of araneophagic salticids has undergone local adaptation to local prey, and there is evidence of predator-prey coevolution. Trade-offs between mating and predatory strategies appear to be important in ant-mimicking and araneophagic species." Ants also show amazing flexibility in behavior.

All but one of the emails I received asked me if I agreed with the author's examples and could I please weigh in on how apt they were. I agreed to do so, and here are half a dozen misleading claims and my comments in brackets. In "The Biology of Belonging," we read statements such as:

  • When you see a group of animals, you may think they have the kind of togetherness that you are missing. But the fact is that animals have a lot of drama in their social groups. [They do, indeed, and the drama changes with variations in ecological and social conditions, and for example, groups or packs of mammals, flocks of birds, and shoals of fishes show marked within species variations.]
  • When a mammal leaves its group, it feels threatened. This motivates it to return to the good feeling of safety in numbers. [This is not necessarily the case. Individuals leave their natal and other groups for a wide variety of reasons, including trying to form their own groups, finding a mate, or because they're not getting what they need from their group mates.]
  • Life in a herd is not all warm and fuzzy. Sticking with the herd means eating food that others have trampled and having their horns in your face. You would rather trot off to a greener pasture, but when you do, you feel like your survival is threatened. [It's true that life isn't always "warm and fuzzy," but a good deal of research shows that group living can be rather amicable and that positive prosocial encounters far outweigh divisive or aggressive interactions.]
  • It may seem like animals have the nice solidarity that you long for, but it’s useful to know that each member of a herd pushes its way toward the center, where it’s safer from predators. When a critter is old, it loses these contests and ends up around the edges, where it’s more easily picked off. Mammals stick with the herd despite the drama because to do so is rewarding. [While social dynamics like this can occur, what's fascinating is that they don't always happen like clockwork, and it's exciting to learn why they do and why they don't, and how ecological and social contexts drive different sorts of encounters. What works in one context might not, and often does not, work in other situations. And the comment about older critters simply isn't true.]
  • The mammalian facts of life may seem harsh, but a reptile’s life is much harsher. Reptiles do not trust their fellow reptile in the way mammals do. [I can't find any data that support this idea, and a reptile expert told me this is a misleading statement. In fact, research shows reptiles experience mammalian-like emotions and show a good deal of individual and between-species variation.]
  • A baboon is expected to risk its life when a grooming partner calls for help. [No researcher I asked knew of any data on this interesting suggestion, but perhaps future research will show that on occasion, this is so, but they're not sure how we'll really know.]

Animal analogies aren't always apt

I hope this brief piece stimulates you to read about the social lives of the fascinating animals with whom we share our planet. There also are excellent, accurate, and easy-to-understand documentaries. Pay particular attention to how they vary from one situation to another because we're learning a lot from ethologists and behavioral ecologists, along with those researchers who are interested in cognitive ethology (how animals' minds work) and cognitive ecology (how animals of the same and other species change their behavior in different ecological settings). It's high time to put misleading myths to rest once and for all. It's essential to separate unsupported beliefs from facts.

Research clearly shows there's no "the mammal, bird, or other vertebrate taxa," and we're also learning more about variation among invertebrates. What keeps many colleagues and me going is that there frequently are no simple answers to why other animals are doing what they're doing. For sure, during more than eight years and thousands of hours of studying wild coyotes, it would have been pretty boring if we really had it all figured out. In fact, when the study ended, there still were numerous unanswered questions, and subsequent research has shed some light on behavior patterns about which we didn't learn or for which we had only half-baked opinions.

All in all, other animals form groups of different sizes and compositions for many reasons, including getting and defending food, acquiring and defending territories, and raising their and others' children. In "The Biology of Belonging," we read, "Common enemies are the glue that bonds a group." This is a good way to put it most of the time, but human and nonhuman groups form and break up for other reasons.

Stay tuned for more on the evolution of sociality and the many ways in which individuals adjust their behavior to current and ever-changing contexts. Nothing is lost, and much is gained when we pay close attention to the myriad ways nonhumans change their behavior by paying close attention to what's happening around them. I'm sure that there is a lot of exciting research coming down the turnpike on the evolution of sociality and the remarkable flexibility and adaptability which numerous animals display. It's incredibly exciting to learn about the other animals—familiar, unfamiliar, and strange—with whom we inhabit our magnificent planet and to come to a more complete understanding of Earth's astounding and precious biodiversity.

1) For more information on coyotes see Coyotes: Dispelling Myths About Who They Are, What They Do. (Some recent media claims about behavior are misleading.) Coyotes: Let's Appreciate America's Song Dog and Social Ecology and Behavior of Coyotes, a lengthy monograph summarizing our fieldwork on coyotes living in the Grand Teton National Park.

3) For more information on other vertebrates and invertebrates Google searches work well. These essays and references therein also contain a lot of information. Sentient Reptiles Experience Mammalian Emotions. (A detailed review of scientific data finds evidence of reptile sentience.) The Emotional Lives of Reptiles: Stress and Welfare Why Fishes Matter: Their Rich Cognitive and Emotional Lives A Tribute to Dr. Victoria Braithwaite and Sentient Fishes Fishes Show Individual Personalities in Response to Stress. (Trinidadian guppies display complex individual and consistent coping strategies.) Fish Show Coordinated Vigilance and Watch Each Other's Backs. (A new study shows fish show reciprocity and provide safety for foraging partners.) Fish Are Sentient and Emotional Beings and Clearly Feel Pain and Balcombe, Jonathan. What a Fish Knows: The Inner Lives of Our Underwater Cousins. Scientific American / Farrar, Straus and Giroux, 2017.

More on invertebrate behavior can be found here and in these essays and references therein: Spider Smarts: Data Show Their Minds Extend Into Their Webs Spider Builds Complex Lifelike Replica Decoys Outside Web. (A spider living in the Peruvian Amazon constructs decoys to scare off predators.) Ants Rescue Sibs From Spider Webs and Surprise Us Once Again. (Harvester ants join chimpanzees and mountain gorillas in the "rescue club.") Ants Build Traps for Grasshoppers, Male Fruit Flies Orgasm Ants Show Organized Healthcare and Treat Wounded Comrades. (This is the first observation of animals routinely treating injured individuals.) and Lonely Ants Die Young: They Don't Know What to Do When Alone. (Socially isolated ants lose digestive functions and suffer due to this loss.)

4) General references and textbooks on animal behavior and behavioral ecology can be found here and here.

Bekoff, Marc. Life Lessons from Dogs, Orcas, Pigs, Cows, Rats, and Chickens. (Numerous animals offer valuable guides for dealing with life's ups and downs.)

Dagg, Anne Innis. The Social Behavior of Older Animals. Johns Hopkins University Press, 2009.


What do you call clearly different sub-groups within a species? - Biology

Next lecture, we shall be talking about speciation. So here we need to cover topics about the nature of species, and discuss how and whether speciation is different from microevolution (evolution within species)?

- What are species?
- How do species differ from each other?
- How many species are there? We will briefly cover species-level biodiversity .


Species "concepts" - What are species?

Darwin in 1859 proved to the world (the reasonable part of it, anyway!) that species evolved, rather than were created. But this made for a difficulty. All of a sudden species weren’t created kinds, with an Aristotelian essence, as previously thought. It then became unclear how species differed, if at all, from other categories. Species evolve from non-species, so where is the dividing line? Darwin hard a hard time with this one, because if species didn’t exist, he could hardly write a book on their origin, could he?!

Darwin’s resolution of this conundrum was to use a pragmatic definition of species - sometimes dismissively called the morphological species concept, in which species were distinguished from races and polymorphic forms by drawing a suitable dividing line in the actual continuum between species and races or forms.

It would be nice to say that there the story ends. Unfortunately, it doesn’t. Species concepts have been for the last 10-20 years a major battleground for systematists, philosophers of biology, and evolutionists. My own view is that Darwin was thinking more clearly than many of the modern contestants, even though his theory of genetics was patently wrong. But not many agree with me (yet!). I will therefore attempt to give you a fairly balanced assessment.

So here are just some of the leading "species concepts", and their strengths and weaknesses.

1) The morphological species concept ( phenetic species conceptalso included)

According to Darwin, species can simply be diagnosed by morphological gaps in the variation between individuals (see diagram above, where the line separates two morphological clusters of individuals). For instance, Darwin regarded Primula veris (the primrose) and Primula elatior (the cowslip) as varieties of the same species because many intermediates or hybrids are found between them. He argued in the same way that the many races of humans were members of the same species. In these cases, it is not easy to find a sensible place to put a dividing line, even though there are clear differences between the forms. Darwin’s ideas were revived by numerical taxonomists in the 1960s, who introduced a multivariate statistical version of the idea, known today as the phenetic species concept.

However, Darwin’s ideas do lead to some problems:

a) Variation within species sometimes leads to morphological gaps. For instance, we have seen that races, subspecies, populations and even morphs within populations are often discrete (i.e. the variation is discontinuous, there are gaps). Nowadays, we would certainly not classify the melanic form of the peppered moth as a different species just because the variation is not continuous.

b) Lack of differences between species: There are often sibling species which (a) are morphologically more or less identical, although genetically different, (b) evolve more or less separately, (c) have little or no hybridization or gene flow between them. Some examples are:

  • willow warbler and chiff-chaff in UK - sing different songs
  • Drosophila fruitflies: D. pseudoobscura and D. persimilis, which differ chromosomally
  • Anopheles mosquitoes, which differ in habitat, biting propensity, and whether they carry malaria

2) The biological species concept

Difficulties with Darwin's concept tempted a number of people to try to redefine species by means of interbreeding. These ideas were first put forward clearly by an entomologist, E.B. Poulton in 1903. Later, Dobzhansky (1937), and, most famously, Mayr (1940, 1942, 1954, 1963, 1970 etc. etc.) carried on and popularized this tradition it was Mayr who named the idea the "biological species concept", thereby unfairly trying to take the high moral ground because anyone else’s species concept was thereafter, of course, "non-biological"!

The biological species concept allows for abundant gene flow within each species, but a lack of hybridization or gene flow betwen species. The lack of gene flow is caused by isolating mechanisms , a term invented by Dobzhansky, but again popularized by Mayr. Because they are not necessarily " mechanisms " in any sense, I prefer the term " reproductive isolation ":

Types of reproductive isolation
A) Pre-mating isolation < or pre-zygotic isolation>
a) Ecological or seasonal isolation - mates do not meet
b) Behavioural (biochemical) isolation - individuals meet but do not attempt mating
c) Mechanical isolation - attempts at mating do not work!

B) Post-mating < orpost-zygotic> isolation
d) Gametic incompatibility - gametes die before fertilization > (note: this is post-mating but pre-zygotic)
e) Hybrid inviability - hybrids have reduced viabilility as zygote or later in development. This may be caused by internal (genomic factors), or because hybrids are not suited to survival for ecological reasons. Hybrids may also have reduced mating propensity, or be disfavoured as mates.
f) Hybrid sterility - hybrids survive and mate as normal, but are partially or completely sterile.
g) Sexual selection against hybrids (studied by Russ Naisbit, a PhD student in my laboratory) - hybrids are healthy and fertile, but disfavoured during mating.

Problems with the biological species concept
a) Does not apply in allopatry. Strictly, the biological species concept only works in sympatry and parapatry, because how can we tell whether two species would intercross if they are allopatric? We can put them together to see if they interbreed, but many sympatric species of ducks, Drosophila, even tigers and lions will interbreed in captivity, though they rarely, if ever, do in the wild.

So when two species are allopatric, we have to guess from their traits - morphology, behaviour, genetics - and their behaviour in captivity, if possible, whether they would interbreed if they were in sympatry. Not very scientific? (This is a problem with all definitions of species that propose a single fundamental essence of species. Given that species originate by evolution, species identity is bound to be more dubious the more time that they have been diverging. Thus species are bound to become less real and more difficult to classify with increasing spans of space (in geography) or time (in the fossil record).

b) Natural hybridization and gene flow between species exists.

Around 10% of birds and butterfly species produce hybrids in the wild, although each species usually does so very rarely (maybe 1/1000 or less). Ducks [SEE OVERHEAD] and other birds of paradise seem particularly prone to hybridization (>50% of species) in the wild, even though most of the time they seem like "good" species. Fewer mammals probably hybridize in Europe, only about 6% of species are known to form hybrids in the wild. However one of these is the world’s biggest animal (ever - beats the dinosaurs hands down): the blue whale, has been recorded hybridizing with its near relative, the fin whale. Not only that, a female hybrid between these two species has been found with a healthy foetus, genetically a backcross. Plants are especially well known for their tendency to hybridize (probably well over 20%), and hybridization is even a major source of speciation by allopolyploidy in this group (see below). For this reason, the biological species concept has never really caught on with botanists.

Hybridization would not matter if genes did not pass between species via hybridization. But we now know that genes DO pass between species, and many species have received genes, or whole mitochondrial genomes from other species. In some cases, flowering plants have even adopted genes from symbiotic bacteria. DNA sequencing has now revealed many, many examples of this kind of horizontal gene transfer between species . Hybridization and gene transfer are today very important topics in conservation and economic biology.

Although the biological species concept has long been accepted by many evolutionary biologists (especially zoologists) as the best species concept, these kinds of problems have led to increasing attacks. Several possible solutions have been proposed.

3) Ecological species concept

Leigh Van Valen, in the 1970s suggested that species were better defined by the types of selection they underwent, or by their ecological niche . Real species, argued Van Valen, are ecologically different.

a) It is at least theoretically possible that some kinds of sibling species might have exactly the same niches. Eventually, this would lead to a probable loss of one of the species through competition, so this problem is perhaps more theoretical than actual.

b) The worst problem for this idea is that species often do have ecological morphs within the species. The cichlid fish Cichlasoma from Cuatro Cienagas, Mexico, has multiple morphs that do different things:

  • one is bottom living, has grinding molariform teeth, and feeds on molluscs
  • another is pelagic, has sharp teeth, and feeds on fish
  • a third has rounded teeth and feeds on algae and detritus

4) Cladistic and phylogenetic species concepts

Recently, most systematists have favoured phylogenetic systematics, in which cladistic classifications. The cladistic movement was founded by Willi Hennig in the 1950s. If higher taxa are defined by means of phylogeny, then so should species, reasoned cladists. This has led to a plethora of cladistic and phylogenetic species concepts. One idea, based on Willi Hennig’s own idea, and supported by Ridley among others is a cladistic species concept:

According to Hennig and Ridley, species are branches in a lineage. When the lineage branches, two new species arise out of the old one, as above, where 5 species result from a phylogeny with two branching (speciation) events. Although there is a morphological discontinuity within the history of species 2, this does not mean the upper and lower portion of species 2 are different species, unless a new branch (in grey) originates at that point. The virtue of this idea to its proponents is that it should apply in history, to fossils, as well as to modern species.

Unfortunately, there are Problems :

a) In practice, phylogenies are unstable hypotheses rather than facts. The branching pattern must be known in order to define species. Cladistic species may therefore be somewhat arbitrary. Supposing the grey branch was unknown, then was suddenly discovered in a small modern population. Now, suddenly, fossil species 2 must be reclassified into two separate species, even though a continuous record of those forms were previously well known. Worse, if the grey lineage has no fossil record, we don’t know where species 2 must be divided.

b) Many island populations may be cladistic side-branches of mainland species yet their establishment does not usually alter the mainland species in any way whatsoever. In fact, this may be true for any population that has been geographically isolated for a few generations. Cladistic species concepts could lead to a lot of new species that are only faintly recognizable.

c) Hybridization, if it occurs between branches, will tend to lead to a lack of clear branching between related pairs of species at some genes. The phylogeny of species may be meaningless under such conditions instead, the phylogeny becomes a mass of "genealogies" at sometimes contradictory genes. Of course one could use some sort of average phylogeny (sometimes called a "consensus" phylogeny) as the "true" species phylogeny, but this kind of averaging is certainly very different from the notion that the species we are looking at have a single true phylogeny.

There are many alternative evolutionaryand phylogenetic species concepts which attempt to answer these problems. For example, various kinds of phylogenetic concept have attempted to incorporate the possibility of gene flow between species. For instance, Cracraft suggests that species have fixed differences at (morphological) "characters", but critics have argued that this would lead to the recognition of many local populations with trivial genetic differences as separate species. It is also a little unclear what one means by "fixed" differences when gene flow will prevent complete fixation. We don’t have time to go through all the species concepts of this sort here, but you can find them in many books (some of my own efforts, encyclopaedia entries with general references, are available from my home page).

5) Rank-free taxonomy, and giving up on species altogether!

Recently, a number of leading phylogenetic systematists have proposed "rank-free" taxonomy, in which species no longer hold a unique position in the taxonomic hierarchy. Proponents of this view argue that the difficulty of assigning a species rank exists because species lack reality as special taxa. Instead, they argue, we should develop a completely new taxonomy based purely on phylogenetic principles, and do away with the Linnean binomial (i.e. two Latin names: genus + species) tradition. The first revision of a taxonomic group without species designations has recently been published in the journal "Systematic Biology" (2000). Whether this idea will catch on is hard to say. If it does, it could cause chaos in biological nomenclature at a time when we badly need taxonomists for studies in biodiversity and conservation. There is a very strong resistance to this idea from among traditional taxonomists, and also from within even the phylogenetic systematists.

My own view is that hybridization and gene flow will wreck the idea of the perfectly hierarchical rank-free taxonomy, especially near the (current) species level, and that species will remain a convenient naming device to classify animals and plants. There must be a certain validity to species, or your bird or plant guides wouldn't be very useful. In some asexual taxa, like brambles and dandelions, it may be somewhat difficult to distinguish "species" from "varieties", but mostly even asexual taxa are easy to divide along species lines. On the other hand, I rather agree that the supposed "reality" of species over and above other higher (genera, families) or lower (subspecies, varieties) taxa has been greatly overemphasised.

Why are there so many species concepts?

What should practising evolutionary geneticists like you do, faced with such a diversity of opinion?

  • Many evolutionary biologists, provided they do NOT work on plants, think the biological species concept is best.
  • Many taxonomists and systematists think that some form of phylogenetic species concept is best, while some profess to get rid of species altogether on the grounds that true phylogenetic taxonomy should be purely hierarchical, and rank-free.
  • Ecologists assume and often use the ecological species concept.

I have my own way of making sense of this debate, with which you may or may not agree. I argue that you can update Darwin’s idea of species without too much difficulty, but take account of modern knowledge of genetics, and thereby solve some of the problems inherent in the other species concepts at the same time.

Species within a region are genetically differentiated populations potentially connected by gene flow. This gene flow may be very low (as in the biological species concept), but it doesn’t have to be negligible. The important thing is that the gene flow is low enough, and the disruptive selection keeping the populations apart is strong enough so that genetic differences between the species are maintained. If the two populations collapse together, because the gene flow outweighs selection, then there will only be a single species.

Species are then clusters of genotypes with discontinuities or gaps between them (a genetic version of Darwin’s morphological concept ). Low levels of gene flow (a lack of Mayr’s pre-mating isolation ) could break up the genotypic and phenotypic differences. However, this gene flow, if it exists, may be balanced by disruptive selection, which may be intrinsic (due to interactions between genes within the hybrids, as in Mayr’s post-mating isolating mechanisms ) or extrinsic (due to the environment, as in Van Valen’s ecological concept ) . Darwin’s morphological concept can thus be related to the ecological and biological concepts: the biological and ecological concepts are explanations of the morphological/genotypic situation of two clusters separated by gaps. Phylogenies obviously have something to do with the whole process. As species diverge more and more, hybridization will be reduced, and a separate branch in the phylogeny emerges from the cross-linking caused by hybridization, and becomes progressively better defined.

Phew! Now that’s over, let’s get on with discussing the interesting things about species.

Genetic differences between species

To study speciation, we need to know how species differ from one another genetically. In general, weherever we look, species differ in ways similar to those of populations or geographic races (see EVOLUTION IN SPACE AND TIME), only more so. Here are some of the ways in which species differ:

a) Morphological differences (see Darwin’s definition, above). Morphology differs between races and populations, as well, of course as already mentioned.

b) Enzyme and molecular differences . Francisco Ayala did detailed surveys with allozymes on Drosophila [SEE OVERHEAD]. Species differ at multiple allozyme loci, subspecies at slightly less loci, and so on down to poplations. We have seen that many hybrid zones separate subspecific forms that differ at multiple genetic loci also, and this and Ayala’s work shows clearly that races and species differ genetically in degree rather than kind. This is as true for mtDNA and other DNA markers as it is for allozymes (see also (g) below). Because multilocus differences are common even between populations and races that noone would want to call species, it is almost certain that speciation also involves multiple locus evolution, and indeed more of it!

c) Chromosomal differences . We have already mentioned human/chimp diffferences (see Chromosomal Evolution), and how common this is in other species that have been studied. Again we can point to subspecies and races that differ chromosomally also, only less so. Chromosomally, species are continuous with races, but usually differ more.

Polyploidy is, however one exception to this gradual differentiation. Polyploidy is a very common feature of plant species differences, and only rarely can be considered polymorphic within species because of the almost universal sterility of diploid X polyploid offspring, which are triploid.

d) Signals used in mating . Sexually-selected colours, tail length in birds, pheromones in moths, other insects, and even mammals are all involved in species recognition as well. In many crickets and grasshoppers, as well as frogs, species-specific sounds are required in fireflies, species recognize each other by means of coded flashes [SEE OVERHEAD].

Again, these kinds differences are quite easily derived from mate choice differences within species, perhaps caused by sexual selection or for ecological reasons of efficiency. Differences between races and species are again in degree rather than kind. There is a controversy as to whether mate choice itself may evolve to "protect species" from gene flow. This would be a true isolating "mechanism". See next lecture.

e) Hybrid inviability and sterility - genomic incompatibility . Sterility and inviability are very common in hybrids. We have already mentioned examples produced by chromosomal differences. Mules (donkey x horse hybrids, which are sterile) are another example.

We know from studies of clines and hybrid zones that multilocus hybrid inviability can occur within species as well as between them. On the other hand, some species almost never mate together, but if they do, the hybrids seem not only viable but fertile. Related species of Darwin’s finches and ducks are an example. Once again, species differ from races only in the degree of hybrid inviability and sterility, not absolutely in kind.

A particularly well known kind of difference is known as Haldane's Rule after its discoverer, J.B.S. Haldane. Haldane's Rule states that when only one sex of the F1 hybrid between species is affected by inviability or sterility, that sex is usually the heterogametic (XY) sex, rather than the homogametic (XX) sex. The rule works in mammals and Diptera (flies) in which the sex-determination is usually male - XY, female - XX as well as in birds and butterflies, in which females are XY and the males are XX. The reason is probably mainly due to recessive effects of genes causing incompatibility on the X chromosome. These genes must be epistatic can you see why?

In other cases, the F1 hybrid between two species may be alright, but backcrosses or F2 crosses produce inviability or sterility. This is known as hybrid breakdown , and may be caused by recessive incompatibility genes (also epistatic) becoming homozygous during these later crosses.

f) Ecological differences . Perhaps the best examples we have of ecological differences between closely-related species are adaptive radiations on islands. Darwin’s finches are well-known. The Hawaiian honeycreepers [SEE OVERHEAD] are even more extraordinary. From finch-like ancestors, they have produced nectarivorous, insectivorous, frugivorous, as well as seed-eating forms.

But we have already discussed under the ecological species concept how ecological differences are found across clines that are under extrinsic selection across an environmental gradient. Once again there is no clear dividing line between races and species in the degree of ecological differentiation.

g) Genealogical differences . As we have seen, when species diverge, their DNA, such as mitochondrial DNA, will also diverge. When a genealogy (the phylogeny of a single gene or stretch of DNA) is estimated, one usually finds that species, and sometimes even races, fall on different branches of the genealogy. An example is given by the Heliconius butterflies, on which own group work, in the figure below.

Heliconius cydno and H. melpomene are closely related species which also occasionally hybridize. They clearly fall on separate branches of this genealogy of the genes CO1 and CO2 of mtDNA. However, it is also true that the melpomene from French Guiana falls on a separate branch of the genealogy from the members of the same species from Panama, and there is a similar deep branching pattern even within Panamanian cydno. Thus, a separate genealogy is not a good guide to separate species status. Other geographic races of Heliconius melpomene have mtDNA genealogies that intermingle with the Panamanian H. melpomene, so not all geographic populations have separate genealogies.

However, in some cases, as in the Drosophila (melanogaster, simulans, sechellia, and mauritiana) genealogies [OVERHEAD], gene genealogies of well-recognized separate species intermingle. In this case two possibilities exist: (1) ancestral polymorphisms -- speciation occurred recently enough so that polymorphisms for genes within each species are retained. (2) interspecific gene transfer -- horizontal gene transfer since the origin of the species has led to an intermingling of the genealogies more recently. These two are difficult to tell apart.

In any case, even at the genealogical level we see intermingling above the species level as well as below. Separate genealogical branches have evolved within some species, as well as between many, perhaps most species. Genealogies of species may be more separate than those of races and populations within species, but there is a lot of overlap.

Genetic differences between species , then are usually inherited at multiple loci, and are on average greater than and involve more genes than (though overlap and blend into) the kinds of differences we see between geographic races, or even morphs in polymorphic populations. There is nothing magic about the species level in terms of genetics, and therefore it would seem most logical and parsimonious (simplest) to use the same microevolutionary forces - selection, drift, mutation - coupled with more time, to explain the evoloution of species, as well as the other kinds of subspecific evolution we have already discussed.

Strictly, biodiversity means the sum total of diversity at all levels of the evolutionary hierarchy, from genetic diversity within populations, between populations, between races, species, genera, and so on, up to ecosystems and biomes. In practice, the species is traditionally viewed as one of the most important level of biodiversity. In view of the difficulty of defining species (above), perhaps this isn't valid?


Some Facts

A wide number of protozoans do not cause any harm, but there are a few that cause diseases in humans.

Trypanosoma brucei causes the African sleeping sickness. Giardia causes diarrhea. They are flagellates.

Another protozoan is Trichomonas vaginalis, a sexually transmitted flagellate that can induce urogenital symptoms in infected women.

Amoebiasis is a gastrointestinal disease caused by Entamoeba histolytica. It also causes dysentery.

Plasmodium is the cause of malaria in humans.

Ciliates feed on bacteria and are often an indicator of good-quality sludge and generally seen in young to medium age sludge. They are important because they eat the bacteria in the sludge and help to clarify the effluent.

Protozoa possess varying characteristics. Scientists consider that animals developed from protozoan ancestors. Modern studies are helping us understand the evolutionary relationship between protozoa and complex multicellular organisms.

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Watch the video: Visual Group Theory, Lecture: Normalizers (November 2021).