Parallel speciation, despeciation and respeciation: implications for species definition

Can the same species arise more than once in different places or at different times? Can a species go extinct by hybridization? If so, can it reappear afterwards? Biologists are used to thinking about species as historical events. They arise once (speciation), exist for a certain time (undergoing stasis or anagenetic change) and then disappear (extinction). Some people even like to think of them as ‘individuals’, although, whether the use of the technical philosophical definition of this word is helpful to many biologists, is perhaps debatable. By and large, our observations of real animal species are not at all incompatible with these ideas. But, recent studies on fishes are suggesting that we may need to rethink our views of the life of a species to include the concepts of parallel speciation, despeciation and respeciation.The ideas I discuss in this paper are not necessarily new, but many fish biologists, like myself, may not have found any particular reason to consider them until recently. There is a very large literature on species concepts, and in a short opinion piece, I could scarcely attempt to do justice to the breadth of the debate or the complexity of the arguments raised. I will focus on issues relating to practical implications of species concepts that have to come to my attention as a fish biologist working on evolutionary questions.     

Species concepts: the basis for controversy and reconciliation

Some of the disputes about species concepts can be resolved through clarification of the conceptual issues. Others are intractable because incompatible preferences are being optimized. According to the current biological consensus species (taxa) are populations rendered cohesive by sex. The philosophical consensus has it that the species and other categories are (abstract) classes, whereas particular species and other taxa are (concrete) individuals (in the ontological sense). Natural kinds are classes that have the properties they do because of laws of nature. Individuals such as species and clades owe their properties to history, not laws of nature; they are not kinds at all and calling them natural kinds is, therefore, grossly misleading. Having the species of taxonomy be equivalent to the species of evolutionary theory facilitates the integration of history and laws of nature within biology. Efforts to define the species category on the basis of similarity create misleading impressions about the laws and mechanisms of speciation processes. A diversity of incompatible species concepts (pluralism) is undesirable because the various kinds of units that are called ‘species’ differ with respect to the underlying laws of nature that make them natural kinds.     

On biological species, species concepts and individuation in the natural world

I am a realist and argue that biological species exist in nature. I also argue that the validity of findings of the many disciplines within the natural sciences employing biological species in their endeavours of inquiry are unequivocally linked to the accuracy of the species used in experiments. Few scientists today see the fundamental importance of taxonomic and systematic studies in both addressing accuracy of diversity and the delineation of species diversity for other areas of science. The basic controversial issues in the debate revolve around opinions regarding the nature of species as either Individuals or Classes, confusion of Species as a taxonomic category and as entities in nature, the varied practitioners studying diversity, a general lack of a Lineage perspective and a gross chauvinistic perspective on the types of data worthy of exposing and delineating diversity. I argue that species in nature are Individuals and form Lineages. As Individuals, they cannot be defined but can only be diagnosed in time. The category Species is a Class with a definition. The difficulties realised by scientists studying biodiversity in ‘defining’ a species hinges upon the fact that as natural entities they cannot be defined. Recognizing and understanding the origins of characters in species is further complicated if one views species in nature as Classes and lacks an appreciation for the Lineage and the origin and retention of traits through time. This forms an interesting paradox that many scientists have fallen victim to wherein species are viewed as Classes (hence definable, but immutable) yet are used to understand the process of descent that involves lineages and Individuals! The pre‐Darwinian Class perspective of species, combined with a common chauvinistic perspective on characters ultimately delays progress and places a ‘glass ceiling’ on species diversity for planet Earth. One resolution to the species and species concept issue is to view the concepts in a hierarchical manner of primary (theoretical) and secondary (operational) concepts. Interestingly, the issue of Individuals versus Classes for naturally occurring entities is much more widespread and exists in many other scientific fields. Thus, a hierarchical perspective of having a primary, nonoperational concept for natural entities and multiple operational concepts serving as ‘tools’ for discovering natural things consistent with the primary concept is a heuristic methodology that is applicable to the advancement of many areas of science.     

GenBank中裂腹鱼类COI基因序列的分子标记有效性

裂腹鱼类(Schizothoracids)分布有复杂的水系格局, 在形态学鉴定时有些鱼种容易混淆。线粒体细胞色素 C 氧化酶亚基 I(CO I)基因是动物学研究中常用的物种分子条形码, 分析 GenBank 数据库中裂腹鱼类 CO I 作为分子标记的有效性, 可以加深理解和认识前人用这些数据所做的研究工作, 也为今后更合理地使用这些数据提供参考依据。本研究对 GenBank 数据库中裂腹鱼类 CO I 基因的分子标记有效性进行分析评估, 通过同源性比对、参考序列间遗传分歧的估算和系统发育关系重建等方法, 判断 GenBank 数据库中裂腹鱼类 CO I 基因序列的同源性、序列所属鱼种鉴定的准确性, 以及序列信息对系统发育关系的解析力。通过对下载的 1431 条序列进行多重比对发现, 有 3 条序列与其他序列存在显著差异, 同源性存疑, 数据信息经 BLAST 相似性搜索和核查确认为, 以 CO I 基因的互补链形式提交的序列, 比对前应先进行互补链转换。全部序列的比对结果显示, GenBank 数据库中裂腹鱼类的 CO I 基因片段序列均为该基因近 5?端至中部的序列。权衡序列的数量和长度后, 舍弃较短的 35 条序列, 保留长度为 527 bp 的 1396 条序列进行分析, 结果共定义了 228 个单倍型, 在有多条序列的鱼种中, 普遍存在种内共享单倍型, 还有 41 个单倍型为种间共享。裂腹鱼类 CO I 单倍型的平均 p-距离为 9.5%, 与鱼类的属级水平相当, 原始、 特化和高度特化类群各自的平均 p-距离值更低, 体现近期辐射演化的特征, 可能与它们随着青藏高原演化成种的历史较短有关。GenBank 中一些裂腹鱼类 CO I 基因序列的鱼种鉴定存在错误, 在使用时应先与参考序列对比, 或从系统发育分析的角度做出判断。总体来看, CO I 基因序列能够有力解析裂腹鱼类各演化等级裂腹鱼类之间的亲缘关系, 可用于分类和演化的初步分析。结合形态学、生态学、线粒体和核基因的多样性及系统发育关系等进行综合分析, 将有助于更准确地界定裂腹鱼种类, 同时也为深入探讨杂交和成种过程等问题奠定基础。     

How behavioural studies contribute to the species problem: a piscine perspective

During the ascendency of ethology, the study of animal behaviour contributed to taxonomic and phyletic issues, but the approach faded in parallel with the waning of systematic studies in general. Systematics and particularly phylogeny has experienced a resurgence with the advent of molecular tools. The understanding of behavioural evolution has benefited from molecular phylogenies. Behaviour's reciprocal contribution, however, currently lies chiefly in resolving the validity of species designation of allopatric species and in potentially helping in the overall classification of species. I review and evaluate the experimental methods favoured in seeking behavioural isolating mechanisms, and the challenge to the species concept when gene trees and species trees disagree. The dynamic situation in the Great Lakes of Africa offers under‐exploited opportunities to test whether behavioural isolating mechanisms evolve in the absence of secondary contact. Given that behaviour is more immediately responsive to changes in the physical and biological environment, behaviour may be the single most salient adaptive feature in speciation events. The species concept is viewed as a fuzzy but nonetheless useful set.     

Identification of microsatellite loci and examination of genetic structure for the endangered springsnails Juturnia kosteri and Pyrgulopsis roswellensis in the Chihuahuan Desert

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Species concepts and speciation of fishes: concluding remarks

The definition of the species category has stimulated more debate than perhaps any other topic in the biological sciences. There are currently more than 22 different species concepts and the debate continues on which concepts apply to all organisms, which concepts are operational and which concepts should be used in specific circumstances. The first major division of the types of concepts depends on whether one views species as constructs that exist for ordering biodiversity and information retrieval (i.e. classes), or views species as ontological individuals that exist in nature. If species are categories that can be defined, then theoretically, a single species can arise more than once in different places or at different times. If, on the other hand, species are individuals, then they are historical events, monophyletic and each species is unique.     

Going,going, gone? Loss of genetic diversity in two critically endangered Australian freshwater fishes,Scaturiginichthys vermeilipinnis and Chlamydogobius squamigenus,from Great Artesian Basin springs at Edgbaston,Queensland, Australia

1. Artesian springs are particularly sensitive freshwater ecosystems, characterized by specialized flora and fauna which, owing to their isolation, are often endemic. Thus, protection of spring habitats and endemic spring biota is important for biodiversity conservation, particularly because human impacts such as invasive species, habitat destruction, and fragmentation can have such devastating effects.
2. This study investigated the mitochondrial DNA (mtDNA) genetic diversity and structure of two critically endangered (IUCN) freshwater fish species: red‐finned blue‐eye Scaturiginichthys vermeilipinnis, and Edgbaston goby Chlamydogobius squamigenus, with the aim of assisting management agencies to establish relocated populations that conserve the genetic integrity and evolutionary potential of both species.
3. 2862 bp from multiple mtDNA genes were amplified from 111 red‐finned blue‐eye individuals (17 from the 1990s and 94 from 2010), and a 660 bp segment of mtDNA cytochrome b was amplified from 111 Edgbaston goby individuals (from 2010). In total, 14 concatenated mtDNA haplotypes were identified in red‐finned blue‐eye and three cytb haplotypes were identified in Edgbaston goby.
4. Overall assessment of the genetic diversity and structure of the endemic fish fauna from the Edgbaston springs revealed low levels of diversity in both species and a loss of haplotypes in red‐finned blue‐eye over time. In addition, both species displayed significant genetic structure: at the spring scale for red‐finned blue‐eye and at the spring group scale for Edgbaston goby. It is concluded that without the appropriate management of relocated populations, such as considering genetic structure and diversity and selecting high quality habitats, these species are at a severe risk of losing evolutionary potential and becoming extinct. This study provides a valuable example for conservation managers of the contribution that population genetic studies can make regarding the adaptive management of endangered species.

Copyright © 2016 John Wiley & Sons, Ltd.     

Assortative mating between adjacent populations of threespine stickleback (Gasterosteus aculeatus)

Abstract –  The idea that sexual selection can lead to rapid evolution of premating isolation among independent populations (speciation) has been controversial, but is rapidly gaining acceptance among many evolutionary biologists as empirical examples accumulate. A survey of male signals and female preferences (mate recognition systems, MRSs) across the contact zone between divergent populations of threespine stickleback ( Gasterosteus aculeatus ) in Conner Creek, WA, revealed a spatial pattern of MRSs that is consistent with speciation via sexual selection. Females from locations that possessed melanic males preferred melanic males whereas females from populations possessing typical mosaic males (red chin, blue iris, and blue-green dorsum) preferred mosaic males. I argue that sensory drive sexual selection, acting through geographically varying spectral properties, is responsible for the observed population differences and premating isolation between the adjacent populations.     

Behavioural plasticity and population connectivity: Contributors to the establishment of new pinniped breeding colonies

1. Understanding the ecological and evolutionary processes that occur during range shift or (re-)colonization is of critical importance for species whose ranges are changing due to human-induced climate change or species such as New Zealand sea lions where their established colonies are significantly declining due to human impacts.
2. The mechanisms underlying colonization are poorly understood. Observations are required to determine the processes that change individual's behaviour associated with colonization, but such observations are rare.
3. Here, the establishment of a new breeding colony of New Zealand sea lions, Phocarctos hookeri, as they recolonized mainland New Zealand, an area from which they had been absent for ~200 years was investigated.
4. There are differences in breeding location behaviour and population connectivity between established and establishing colonies of New Zealand sea lions. The recolonizing population is more dispersed with breeding locations that change annually and have more connections with other populations compared with established colonies and populations.
5. The establishment of a new colony and the greater numbers of resightings between colonies means that for species' management, considerably more public education, habitat management, and protection is needed to ensure the safe return of New Zealand sea lions back on to mainland New Zealand.

     

Fishes that rule the world: circumtropical distributions revisited

Briggs ( 1960 ) published the first checklist of circumtropical fishes with 107 species. This work served for a half century as the most comprehensive checklist of globally distributed fishes, but the intervening years witnessed many discoveries, and molecular data have changed the way we evaluate species. Here, we update the list guided by taxonomic revisions, phylogenies, phylogeographic data and DNA barcodes. The resulting list now includes 284 species. The dramatic increase is primarily due to two trends: (i) continued oceanic exploration leading to range revisions and species discoveries and (ii) public databases such as FishBase and the Catalogue of Fishes make range data more accessible. Five species were removed from the list as closer scrutiny revealed multiple taxa, 14 were removed due to updated range information, and 35 more are suspected to be species complexes. The species listed here are mostly pelagic and bathypelagic fishes. Euryhaline, anadromous, catadromous, freshwater, and with few exceptions, reef fishes do not achieve global distributions. The most species‐rich family of marine fishes (Gobiidae) is absent. The fishes with the longest pelagic larval stage (Anguillidae) are absent. In contrast, requiem sharks (Carcharhinidae), tunas (Scombridae), jacks (Carangidae), remoras (Echeneidae) and especially lanternfishes (Myctophidae) have multiple representatives. The combined evidence indicates that high mobility as an adult is a key requirement to achieve a global distribution. Many others are members of monotypic genera or families, indicating old lineages that did not diversify. We conclude that global ranges may promote persistence over evolutionary timescales, but also reduce opportunities for speciation.     

大港湾浮游动物调查报告

本文对大港湾浮游动物调查的结果进行了研究分析，共记录各类浮游动物７９种，划分有三个生态类群，以沿岸低盐暖水性类群和广盐暖水性类群为主体，体现亚热带性质的群落结构特点，总生物量和总个体数量均较高，分布趋势基本一致，南部水域高于北部水域，外侧水域高于内侧水域，高生物量区分布在东南侧。据大港湾浮游动物的多样性指数和丰富度等指标的分析结果。认为：大港湾未受污染，浮游动物种类丰富，多样性好，发展网箱养殖前景     

Effects of fish species richness and assemblage composition on stream ecosystem function

Abstract –  Biodiversity is declining across aquatic ecosystems because of biological invasions and species extinctions. Because fishes have pervasive effects on ecosystems through species-specific food web interactions, alterations to species and functional richness, and composition of natural assemblages could have negative effects on aquatic ecosystem function. In this study, I tested the effects of fish species and functional richness, and assemblage composition on primary production (PPR), benthic invertebrate density, and benthic particulate organic matter (BPOM) in a 42-day experiment in artificial stream mesocosms. I found that fish species richness and assemblage composition were important predictors of PPR in stream mesocosms. However, the effect of species richness on PPR increased with time, suggesting that richness-related effects might strengthen as the magnitude of community-level interactions increases in ecosystems. There was no effect of fish species or functional richness or assemblage composition on benthic invertebrate densities or BPOM. These data provide additional support that fishes can be important regulators of ecosystem function in aquatic systems, and suggest that positive effects of fishes on ecosystems can be strengthened by increased species richness and composition of the assemblage. This study broadens the applicability of the biodiversity ecosystem-function literature to a new suite of taxa, supporting the overall hypothesis that ecosystem functions and services are likely to decline in response to species extinctions.     

Quantifying morphological and genetic variation of sympatric populations to guide conservation of endangered,micro‐endemic springsnails

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Molecular phylogenetic relationship of Tetraodon pufferfish based on mitochondrial DNA analysis

Pufferfishes belonging to the genus Tetraodon form one of the largest groups in the family Tetraodontidae. This group consists of more than 20 species distributed across freshwater, as well as brackish and coastal waters, of Africa and Southeast Asia. However, their phylogenetic and evolutionary relationships are still ambiguous. In the present study, mitochondrial genes encoding 16S rRNA and cytochrome b were sequenced for 17 Tetraodon species collected from various areas mentioned above. Supermatrix analysis based on the complete sequences of the two genes from Tetraodon species was performed using a tree with 50 tetraodontid species (including 7 Tetraodon species) as a backbone. The obtained phylogenetic tree classified Tetraodon species into three groups, correlating well with their habitats, such as Asian freshwater, Asian brackish water, and African freshwater. We also showed that salinity tolerance of Asian freshwater species T. cochinchinensis was apparently lower than that of Asian brackish water species T. nigroviridis, suggesting that the speciation of Tetraodon species in the Asian freshwater group was caused by the molecular evolution associated with osmotic regulation.     

Genetic diversity and connectivity patterns of harvested and aquacultured molluscs in estuaries from Asturias (northern Spain). Implications for management strategies

Estuaries are among the most important habitats of coastal areas. However, they are significantly affected by human activities worldwide, threatening their resources and the commercial uses depending on them. Fisheries and aquaculture are some of the main factors affecting the estuarine ecosystems today. In this work, we pursue the aims of genetically identifying the cultured and harvested oyster and razor clam species inhabiting Asturian estuaries (Eo, Ribadesella and Villaviciosa) and describing the genetic diversity and patterns of genetic connectivity between those species in these estuaries. The results revealed the almost complete dominance of the introduced Crassostrea gigas as the species that supports the oyster's production in Asturias with a striking diversity of gene pools in wild environments (Ría de Villaviciosa and Ribadesella) which significantly exceeds the diversity found in the hatcheries seeds commonly used for culturing. Moreover, we detected two different species of Ensis sp. inhabiting the Asturian estuaries: Ensis ensis inside Ría del Eo and Ensis directus, an invasive species, in Ría de Villaviciosa. Significant genetic differentiation between estuaries for the exotic oyster C. gigas and also for the native razor clam Solen marginatus were found. These results suggest Asturian estuaries are not a single management unit for some species and thus prevention must be taken for avoiding intentional or human‐mediated translocations among them. Biodiversity monitoring for discovering newcomer invasive species, measures for environmental recovery of these ecosystems and strict controls to avoid increasing of harvesting pressures are also a necessity to improve the management of these relevant ecosystems.     

Population prioritization for conservation of imperilled warmwater fishes in an arid‐region drainage

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When alien catfish meet—Resource overlap between the North American Ictalurus punctatus and immature European Silurus glanis in the Arno River (Italy)

Due to the increasing globalisation and ongoing introduction of alien species specifically regarding European freshwater ecosystems, native and already present alien species will be confronted with competitors with unknown outcomes. One such case is the situation of the European catfish Silurus glanis introduced in the Arno River (Central Italy), a species sought after by anglers, which is facing competition from the later introduced alien North American channel catfish Ictalurus punctatus. Large catfish species are highly valued among anglers, but their interspecific interactions and potential ecosystem-level impacts are still poorly known. We used stomach contents and stable isotope analyses to study niche partitioning between these two alien catfish species, coexisting in the Arno River. The results suggest partial niche segregation, with immature S. glanis showing a narrower dietary and isotopic niche and a slightly higher trophic position than I. punctatus. Monitoring the catfish population sizes, trophic niches and effects on lower trophic levels are essential for future management and mitigation of their potential impacts on invaded freshwater ecosystems.     

隆头鱼科分类学研究进展

隆头鱼科是体形最为分化、体色最为多变的一个类群,其所包含的种类数位居海洋鱼类第2位。尽管经历了260多年的分类研究,隆头鱼科在分类单元和物种鉴定方面仍存在许多争论和疑问。回顾了隆头鱼科分类学发展史,总结了系统发育学的研究成果,描述了隆头鱼科关键分类特征和基础生物学,概述了几个分类较为复杂的主要属的研究进展,根据分子系统发育,推测几个主要属为复系群,是颌骨摄食功能进化导致种间显著遗传分化的结果。同时,参考1750—2017年期间的文献资料,考证和修订了中国隆头鱼的同物异名和错误命名,厘定中国隆头鱼科有38属150种,并提出我国需要广泛深入的开展隆头鱼科物种的普查和鉴定研究工作及利用分子生物学技术开展隆头鱼亲缘地理学的研究建议,为隆头鱼的起源、物种多样性、分布格局成因以及在海洋生态系统中的功能研究提供基础数据及理论研究参考。     

Allochrony as a potential driver for reproductive isolation in adaptive radiations of European whitefish ecomorphs

In northern Fennoscandian lakes, monophylogenetic lineages of postglacial fishes are radiating into several adaptive forms, but the speciation process is still at an incipient stage. The speciation process has received increased attention over the years, but the underlying mechanisms and drivers are still debated and poorly understood. European whitefish (Coregonus lavaretus [L.]) is the most abundant fish species in these lakes and has evolved into several ecomorphs adapted to different trophic niches and habitats. Genetic divergence has been observed among these ecomorphs, but the mechanism(s) responsible for the ongoing build-up of reproductive isolation has still to be revealed. As these systems are young in evolutionary time (<10 kyr), prezygotic and postzygotic extrinsic isolation mechanisms are thought to be more likely to contribute to the reproductive isolation than intrinsic isolation mechanisms. We determined the gonadosomatic index (GSI) of three ecomorphs in two replicated lake systems and used GSI as a proxy to investigate the prezygotic isolation mechanism, allochrony, as a driving factor of divergence in this adaptive radiation of whitefish. We found that the three ecomorphs differed in GSI values within and between lakes, suggesting different spawning times of the ecomorphs. We also show that males of one ecomorph had equal onset of maturity as another ecomorph, giving novel insights into the ongoing gene flow observed between ecomorphs. The result supports allochrony as a driver for the divergence process of whitefish ecomorphs, but more evidence is still needed to rule out that the three ecomorphs make use of different spawning grounds.