Species limits and taxonomy in birds (2 Viewers)

[Jim LeNomenclatoriste]

Kevin Winkler & Pamela C. Rasmussen (2021). Species limits and taxonomy in birds. Ornithology, ukab017

Species limits and taxonomy in birds

Abstract. Despite the acknowledged importance of defining avian species limits to scientific research, conservation, and management, in practice, they often rem

academic.oup.com

Abstract
Despite the acknowledged importance of defining avian species limits to scientific research, conservation, and management, in practice, they often remain contentious. This is true even among practitioners of a single species concept and is inevitable owing to the continuous nature of the speciation process, our incomplete and changing understanding of individual cases, and differing interpretations of available data. This issue of Ornithology brings together several papers on species limits, some more theoretical and general, and others case studies of specific taxa. These are viewed primarily through the lens of the biological species concept (BSC), by far the most widely adopted species concept in influential ornithological works. The more conceptual contributions focus on the importance of the integrative approach in species delimitation; the importance of considering selection with the increasing use of genomic data; examinations of the effectiveness of the Tobias et al. character-scoring species limits criteria; a review of thorny issues in species delimitation using examples from Australo-Papuan birds; and a review of the process of speciation that addresses how population divergence poses challenges. Case studies include population genomics of the American Kestrel (Falco sparverius); an integrative taxonomic analysis of Graceful Prinia (Prinia gracilis) that suggests two species are involved; and a reevaluation of species limits in Caribbean Sharp-shinned Hawk (Accipiter striatus) taxa.

Well, well, well

 

[Mysticete]

Kevin Winkler & Pamela C. Rasmussen (2021). Species limits and taxonomy in birds. Ornithology, ukab017

Species limits and taxonomy in birds

Abstract. Despite the acknowledged importance of defining avian species limits to scientific research, conservation, and management, in practice, they often rem

academic.oup.com

Abstract
Despite the acknowledged importance of defining avian species limits to scientific research, conservation, and management, in practice, they often remain contentious. This is true even among practitioners of a single species concept and is inevitable owing to the continuous nature of the speciation process, our incomplete and changing understanding of individual cases, and differing interpretations of available data. This issue of Ornithology brings together several papers on species limits, some more theoretical and general, and others case studies of specific taxa. These are viewed primarily through the lens of the biological species concept (BSC), by far the most widely adopted species concept in influential ornithological works. The more conceptual contributions focus on the importance of the integrative approach in species delimitation; the importance of considering selection with the increasing use of genomic data; examinations of the effectiveness of the Tobias et al. character-scoring species limits criteria; a review of thorny issues in species delimitation using examples from Australo-Papuan birds; and a review of the process of speciation that addresses how population divergence poses challenges. Case studies include population genomics of the American Kestrel (Falco sparverius); an integrative taxonomic analysis of Graceful Prinia (Prinia gracilis) that suggests two species are involved; and a reevaluation of species limits in Caribbean Sharp-shinned Hawk (Accipiter striatus) taxa.

Well, well, well

If anyone can summarize what these papers are about, that would be great, since I don't have access to this journal for recent articles

 

[Snapdragyn]

Ooooh, I want the whole thing!

 

[Jim LeNomenclatoriste]

If anyone can summarize what these papers are about, that would be great, since I don't have access to this journal for recent articles

Even with sci-hub ?

 

[Jim LeNomenclatoriste]

If anyone could send it to us please, you will be a sweetheart

 

[MJB]

If anyone could send it to us please, you will be a sweetheart

Presumably you've got at least this, Jim?
MJB

https://watermark.silverchair.com/ukab017.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsEwggK9BgkqhkiG9w0BBwagggKuMIICqgIBADCCAqMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM73dgBwjEuI5XhDUhAgEQgIICdPqfEoLHiuIXPzP31vtMSv5abrAOIpyAbsJLEFnz24rvZJc5GbdHbmgcmPjbN_2JolU11fjEucn0gVsnMEsaHOZWQE3bSxvLvhU3cvDvUmZqIuiKzP_aMallEHVvaC1irBwA0_8FFe8NFuoPyq6U-JbtMQm3ie-Z-ak8f8O1K0fX7ykVKLhrp3wyaB0z2sleyeFXv81jptnfA4v2Q7aDWHe90EKhkJKTQtRH0hnFbOAmLg4i8HrGaMWrwx2TY6OSNiRM8qrORJ2fGAmTJQ1CBSmSa_I1Yqp9I_FQ_0Q-LvEXA9Dt5XMJK20tMvhb52GnvFFIx0uQhFr9op1a9kqjKzmAU4s0rAtJfQIOtUJAyPg9A8UrgURqkWBCYaIb6XrP6EqHvgvZTTGI-BPjRX1sWBSVTrm54ZChzxLYNzhk4P1IYGutIsHyzRiPKwASQh1rzYBe9P4B1trLXn5224UHWg8wiG_RXOls4NrrQB0FagkrfYKeMmr2H8g3suFiRVdCGuR5CZrp__U1wn2j-aDom-SzPsKVBkv-5pnp79TVQgDLuGzy2MqxqGIX549Zh_MMxYN1O21osiGVsQ80MD5X-E0uGLOa_OwHlgT8wSlv_61-C7Cg-bs7Lw2IEIHQWTRe8ul8pXWCVpOTycjHXhdYozcvx5K8w5gU3EvYBxeqsh9YbqHd8-0HeG_JDrjCADu8s7bn9y5U8Zy3tnRbW2umVyjvdzMw2eGnBcGJkDUf69z78ZnkON-ELaQOna2Wq6JdgxYuInjdIJDYglD7gtmeEg_QV_RD2UWr4snQGNaxfTb05huzbjBN89UW7o6sOWiJlDbNypc

 

[Jim LeNomenclatoriste]

Presumably you've got at least this, Jim?
MJB

https://watermark.silverchair.com/ukab017.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsEwggK9BgkqhkiG9w0BBwagggKuMIICqgIBADCCAqMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM73dgBwjEuI5XhDUhAgEQgIICdPqfEoLHiuIXPzP31vtMSv5abrAOIpyAbsJLEFnz24rvZJc5GbdHbmgcmPjbN_2JolU11fjEucn0gVsnMEsaHOZWQE3bSxvLvhU3cvDvUmZqIuiKzP_aMallEHVvaC1irBwA0_8FFe8NFuoPyq6U-JbtMQm3ie-Z-ak8f8O1K0fX7ykVKLhrp3wyaB0z2sleyeFXv81jptnfA4v2Q7aDWHe90EKhkJKTQtRH0hnFbOAmLg4i8HrGaMWrwx2TY6OSNiRM8qrORJ2fGAmTJQ1CBSmSa_I1Yqp9I_FQ_0Q-LvEXA9Dt5XMJK20tMvhb52GnvFFIx0uQhFr9op1a9kqjKzmAU4s0rAtJfQIOtUJAyPg9A8UrgURqkWBCYaIb6XrP6EqHvgvZTTGI-BPjRX1sWBSVTrm54ZChzxLYNzhk4P1IYGutIsHyzRiPKwASQh1rzYBe9P4B1trLXn5224UHWg8wiG_RXOls4NrrQB0FagkrfYKeMmr2H8g3suFiRVdCGuR5CZrp__U1wn2j-aDom-SzPsKVBkv-5pnp79TVQgDLuGzy2MqxqGIX549Zh_MMxYN1O21osiGVsQ80MD5X-E0uGLOa_OwHlgT8wSlv_61-C7Cg-bs7Lw2IEIHQWTRe8ul8pXWCVpOTycjHXhdYozcvx5K8w5gU3EvYBxeqsh9YbqHd8-0HeG_JDrjCADu8s7bn9y5U8Zy3tnRbW2umVyjvdzMw2eGnBcGJkDUf69z78ZnkON-ELaQOna2Wq6JdgxYuInjdIJDYglD7gtmeEg_QV_RD2UWr4snQGNaxfTb05huzbjBN89UW7o6sOWiJlDbNypc

The longest password of the universe 🤣🤣🤣

But the link don't work unfortunately

 

[MJB]

The longest password of the universe 🤣🤣🤣

But the link don't work unfortunately

It did for me, but only when I clicked on a link on the main page to open the link on another page. That came up with a seemingly identical page, but the download arrow worked. I'll pass the summary paper directly to you.
MJB

 

[suluhornbill]

Can share the papers? I already try with sci-hub and also the link, but with no success.
Really appreciate it.

 

[MJB]

Can share the papers? I already try with sci-hub and also the link, but with no success.
Really appreciate it.

If your request is addressed to me, open a conversation (click on the envelope near the top right & select 'Start a new Conversation'), and include your email address.
MJB

 

[Peter Kovalik]

José M. Padial & Ignacio De la Riva. A paradigm shift in our view of species drives current trends in biological classification. Biol. Rev. (2021), 96, pp. 731–751. https://doi.org/10.1111/brv.12676

Abstract:

Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life. Species delimitation now consists of determining which populations belong to which individual phylogenetic lineage. This requires inferences on the process of lineage splitting and divergence, a process to which we have only partial access through incidental evidence and assumptions that are themselves subject to refutation. This approach is not free of problems, as horizontal gene transfer, introgression, hybridisation, incorrect assumptions, sampling and methodological biases can mislead inferences of phylogenetic lineages. Increasing precision is demanded through the identification of both sister relationships and processes blurring or mimicking phylogeny, which has triggered, on the one hand, the development of methods that explicitly address such processes and, on the other hand, an increase in geographical and character data sampling necessary to infer/test such processes. Although our resolving power has increased, our knowledge of sister relationships – what we designate as species resolution – remains poor for many taxa and areas, which biases species limits and perceptions about how divergent species are or ought to be. We attribute to this conceptual shift the demise of trinominal nomenclature we are witnessing with the rise of subspecies to species or their rejection altogether; subspecies are raised to species if they are found to correspond to phylogenetic lineages, while they are rejected as fabricated taxa if they reflect arbitrary partitions of continuous or non‐hereditary variation. Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation; local variation is best preserved by focusing on biological processes generating ecosystem resilience and diversity rather than by formally naming diagnosable units of any kind. Since many binomials still designate complexes of species rather than individual species, many species have been discovered but not named, geographical sampling is sparse, gene lineages have been mistaken for species, plenty of species limits remain untested, and many groups and areas lack adequate species resolution, we cannot avoid frequent changes to classifications as we address these problems. Changes will not only affect neglected taxa or areas, but also popular ones and regions where taxonomic research remained dormant for decades and old classifications were taken for granted.

 

[DMW]

Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation;

Perhaps the full paper discusses, but doesn't this statement both contradict the entire premise of their own argument that species level taxonomy is often arbitrary or based on too little data, and ignore the fact that many of the most endangered "lineages" are insular populations with no gene flow?
In other words, taking an arbitrary decision about whether, say, an Acrocephalus on a remote Pacific island is a species or sub-species, leads to you either ignoring it or prioritising it as a conservation priority.

 

[njlarsen]

If you agree to their assumption that any lineage without gene flow is a species, then that subspecies disappears because to them it is a species.

The summary paper from Ornithology argued that the biological species concept remains the starting point, so there is a difference in paradigm between them and this latest paper.

Niels

 

[jts1882]

Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation;

The IOC currently recognises 26k distinct species or subspecies taxa. If this recommendation was followed through how many species would there be? It would be a big showdown of lumpers and splitters.

 

[jurek]

I think that taxonomy and conservation effort should be determined mostly by genetic difference.

• It became practical with the practical DNA testing, and is already published for growing number of species/subspecies,
• It conserves precisely what cannot be brought back once it disappears because of Man's action: unique DNA sequences created by evolution
• It recognizes the additional significance of unique lineages (unique genera, families or orders like Kagu or Kakapo or Shoebill) which are traditionally treated the same as any species.
• It avoids the false dichotomy: worthy / not worthy of conservation which does not match the continuous nature of evolution,
• It is not swayed by human perception of unique characters, e.g. different coloration or voice which may be not important for ecology or birds own mate choice, or different bill size which could change very fast in evolution, or clinal variation which ceases to be clinal after some populations go extinct from man-made actions.
• It does not depend on scientific assumptions which are essentially poorly or not verifiable, e.g. whether a parapatric taxa would interbreed, how much gene flow is allowed between good species, or whether separate evolutionary lineages would / would not merge if they come back into contact.
• It does away with wasting time on discussing essentially man-made concepts and ideas of taxonomy,
• It removes the individual researchers' temptation to split mostly to give more recognition to a taxon.

A similar proposal was made by ZSL as 'EDGE' or evolutionary distinct lineages, but that was based more on taxonomy uniqueness than directly genetic uniqueness.

 

[THE_FERN]

I think that taxonomy and conservation effort should be determined mostly by genetic difference.

• It became practical with the practical DNA testing, and is already published for growing number of species/subspecies,
• It conserves precisely what cannot be brought back once it disappears because of Man's action: unique DNA sequences created by evolution
• It recognizes the additional significance of unique lineages (unique genera, families or orders like Kagu or Kakapo or Shoebill) which are traditionally treated the same as any species.
• It avoids the false dichotomy: worthy / not worthy of conservation which does not match the continuous nature of evolution,
• It is not swayed by human perception of unique characters, e.g. different coloration or voice which may be not important for ecology or birds own mate choice, or different bill size which could change very fast in evolution, or clinal variation which ceases to be clinal after some populations go extinct from man-made actions.
• It does not depend on scientific assumptions which are essentially poorly or not verifiable, e.g. whether a parapatric taxa would interbreed, how much gene flow is allowed between good species, or whether separate evolutionary lineages would / would not merge if they come back into contact.
• It does away with wasting time on discussing essentially man-made concepts and ideas of taxonomy,
• It removes the individual researchers' temptation to split mostly to give more recognition to a taxon.

A similar proposal was made by ZSL as 'EDGE' or evolutionary distinct lineages, but that was based more on taxonomy uniqueness than directly genetic uniqueness.

I guess I broadly agree but one has to realise that a lot of genetic uniqueness has no phenetic significance. You've junk DNA and DNA under no or v little selective pressure ("neutral"). E.g. apparently Paris japonica has the largest known genome with 149 billion base pairs cf 3 for humans. It's a value judgement as to how much of the accumulated history has value: a lot of "junk" is still a lot and is raw material for "meaningful" evolution. These considerations really come into play when you try to decide "how different" 2 things actually are.

It's wrong to believe that genetic characters are a panacea. There are lots more of them and you can use clock assumptions to age them but otherwise they have much the same problems as any other characters.

An enlightened view would value the preservation of culture such as shown by chimpanzees too: many of us seem to think this is important in the human sphere... Culture may have little to do with genetics (the Jewish priesthood aside)

 

[jurek]

That is why genetic distance is measured by percentage of difference, not single genetic characters (which can be as misleading as phenological characters).

To paraphrase the saying about democracy: genetic difference is not perfect, but still more fair than other methods.

While culture is interesting, it is not usually relevant to birds.

 

[Peter Kovalik]

Leo Joseph, Species limits in birds: Australian perspectives on interrelated challenges of allopatry, introgression of mitochondrial DNA, recent speciation, and selection, Ornithology, 2021;, ukab012, https://doi.org/10.1093/ornithology/ukab012

Abstract:

Four main challenges that can underpin ongoing, intransigent debates about species limits in birds are reviewed: allopatry (population subdivision vs. speciation), geographically widespread introgression of mitochondrial DNA (mtDNA), recent speciation, and selection. Examples from birds of the Australian region show how these challenges, their interplay, and the molecular-phenotypic discordance they generate can clarify or mislead species limits. Examples of how phylogenetic frameworks help reject or retain hypotheses of species limits under these challenges are given. Although mtDNA’s strengths and limitations are well known, an underappreciated limitation of mtDNA is geographically widespread introgression that homogenizes mtDNA diversity across species, subspecies, or population boundaries and across hundreds of kilometers. The resulting discordance between mtDNA and phenotype can be profound. If undetected, the setting of species limits and evolutionarily significant units are misled. An example shows how recent genomic analyses can detect and solve the problem. Other examples concern legacy mtDNA-only datasets. These are often essentially unfinished studies leaving residual uncertainty in species limits. Examples illustrate when the possibility of large-scale introgression across species boundaries needs to be considered, and how genomic scale data offer solutions. Researchers must carefully parse 3 questions: has there been introgression of mtDNA and, if so, which population genetics-based driver has caused introgression, and do species limits need altering? Understanding of allopatry, mtDNA introgression, recent speciation, and selection must be properly integrated if species limits are to be robustly understood and applied with maximum benefit in downstream applications such as conservation and management.

 

[Peter Kovalik]

Joseph A Tobias, Paul F Donald, Rob W Martin, Stuart H M Butchart, Nigel J Collar, Performance of a points-based scoring system for assessing species limits in birds, Ornithology, 2021;, ukab016, https://doi.org/10.1093/ornithology/ukab016

Abstract:

Species are fundamental to biology, conservation, and environmental legislation; yet, there is often disagreement on how and where species limits should be drawn. Even sophisticated molecular methods have limitations, particularly in the context of geographically isolated lineages or inadequate sampling of loci. With extinction rates rising, methods are needed to assess species limits rapidly but robustly. Tobias et al. devised a points-based system to compare phenotypic divergence between taxa against the level of divergence in sympatric species, establishing a threshold to guide taxonomic assessments at a global scale. The method has received a mixed reception. To evaluate its performance, we identified 397 novel taxonomic splits from 328 parent taxa made by application of the criteria (in 2014‒2016) and searched for subsequent publications investigating the same taxa with molecular and/or phenotypic data. Only 71 (18%) novel splits from 60 parent taxa have since been investigated by independent studies, suggesting that publication of splits underpinned by the criteria in 2014–2016 accelerated taxonomic decisions by at least 33 years. In the evaluated cases, independent analyses explicitly or implicitly supported species status in 62 (87.3%) of 71 splits, with the level of support increasing to 97.2% when excluding subsequent studies limited only to molecular data, and reaching 100% when the points-based criteria were applied using recommended sample sizes. Despite the fact that the training set used to calibrate the criteria was heavily weighted toward passerines, splits of passerines and non-passerines received equally strong support from independent research. We conclude that the method provides a useful tool for quantifying phenotypic divergence and fast-tracking robust taxonomic decisions at a global scale.

 

[Snapdragyn]

José M. Padial & Ignacio De la Riva. A paradigm shift in our view of species drives current trends in biological classification. Biol. Rev. (2021), 96, pp. 731–751. https://doi.org/10.1111/brv.12676

Abstract:

Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life. Species delimitation now consists of determining which populations belong to which individual phylogenetic lineage. This requires inferences on the process of lineage splitting and divergence, a process to which we have only partial access through incidental evidence and assumptions that are themselves subject to refutation. This approach is not free of problems, as horizontal gene transfer, introgression, hybridisation, incorrect assumptions, sampling and methodological biases can mislead inferences of phylogenetic lineages. Increasing precision is demanded through the identification of both sister relationships and processes blurring or mimicking phylogeny, which has triggered, on the one hand, the development of methods that explicitly address such processes and, on the other hand, an increase in geographical and character data sampling necessary to infer/test such processes. Although our resolving power has increased, our knowledge of sister relationships – what we designate as species resolution – remains poor for many taxa and areas, which biases species limits and perceptions about how divergent species are or ought to be. We attribute to this conceptual shift the demise of trinominal nomenclature we are witnessing with the rise of subspecies to species or their rejection altogether; subspecies are raised to species if they are found to correspond to phylogenetic lineages, while they are rejected as fabricated taxa if they reflect arbitrary partitions of continuous or non‐hereditary variation. Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation; local variation is best preserved by focusing on biological processes generating ecosystem resilience and diversity rather than by formally naming diagnosable units of any kind. Since many binomials still designate complexes of species rather than individual species, many species have been discovered but not named, geographical sampling is sparse, gene lineages have been mistaken for species, plenty of species limits remain untested, and many groups and areas lack adequate species resolution, we cannot avoid frequent changes to classifications as we address these problems. Changes will not only affect neglected taxa or areas, but also popular ones and regions where taxonomic research remained dormant for decades and old classifications were taken for granted.

DOI not found & pdf link only opens a blank page.