Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species

Heredity ◽  
2021 ◽  
Author(s):  
Sofia L. Mendes ◽  
Miguel P. Machado ◽  
Maria M. Coelho ◽  
Vitor C. Sousa
Keyword(s):  
Genomic Data ◽  
Freshwater Species ◽  
Demographic Modelling

scholarly journals Population genomics data supports introgression between western Iberian Squalius freshwater fish species

2019 ◽  
Author(s):  
Sofia L. Mendes ◽  
Maria M. Coelho ◽  
Vitor C. Sousa
Keyword(s):  
Gene Flow ◽  
Freshwater Fish ◽  
Population Genomics ◽  
Genotyping By Sequencing ◽  
Population Divergence ◽  
Freshwater Species ◽  
Genomic Approach ◽  
Demographic Modelling ◽  
Paraphyletic Group ◽  
First Time

AbstractIn freshwater fish, processes of population divergence and speciation are often linked to the geomorphology of rivers and lakes that isolate populations. However, current geographical isolation does not necessarily imply total absence of gene flow during the divergence process. Here, we focused on four species of the genus Squalius in Portuguese rivers: S. carolitertii, S. pyrenaicus, S. aradensis and S. torgalensis. Previous studies based on eight nuclear and mitochondrial markers revealed incongruent patterns, with nuclear loci suggesting that S. pyrenaicus was a paraphyletic group since its northern populations were genetically closer to S. carolitertii than to its southern populations. For the first time, we successfully applied a genomic approach to the study of the relationship between these species, using a Genotyping by Sequencing (GBS) approach. Our results revealed a species tree with two main lineages: (i) S. carolitertii and S. pyrenaicus; (ii) S. torgalensis and S. aradensis. Regarding S. carolitertii and S. pyrenaicus, we found evidence for past introgression between the two in the northern part of S. pyrenaicus distribution. This introgression reconciles previous mitochondrial and nuclear incongruent results and explains the apparent paraphyly of S. pyrenaicus. Our demographic modelling estimates are consistent across models, suggesting that the northern populations of S. pyrenaicus received a contribution of approximately 90% from S. carolitertii and 10% from southern S. pyrenaicus. This illustrates that even in freshwater species currently allopatric, we are able to detect past gene flow events in present-day genomes, suggesting speciation is more complex than simply allopatric.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

Bonobo population dynamics: Past patterns and future predictions for the Lola ya Bonobo population using demographic modelling

2018 ◽  
Author(s):  
Lisa J. Faust ◽  
Claudine André ◽  
Raphaël Belais ◽  
Fanny Minesi ◽  
Zjef Pereboom ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Pan Troglodytes ◽  
Growth Trajectories ◽  
Demographic Model ◽  
Pan African ◽  
Demographic Modelling ◽  
Projected Changes ◽  
Demographic Patterns ◽  
Future Population ◽  
Future Growth

Wildlife sanctuaries rescue, rehabilitate, reintroduce and provide life-long care for orphaned and injured animals. Understanding a sanctuary’s population dynamics—patterns in arrival, mortality and projected changes in population size—allows careful planning for future needs. Building on previous work on the population dynamics of chimpanzees (Pan troglodytes) in sanctuaries of the Pan African Sanctuary Alliance (PASA; Faust et al. 2011), this chapter extends analyses to the only PASA bonobo sanctuary. Its authors analysed historic demographic patterns and projected future population dynamics using an individual-based demographic model. The population has been growing at 6.7 per cent per year, driven by arrivals of new individuals (mean = 5.5 arrivals per year). Several model scenarios projecting varying arrival rates, releases and breeding scenarios clarify potential future growth trajectories for the sanctuary. This research illustrates how data on historic dynamics can be modelled to inform future sanctuary capacity and management needs. Les sanctuaires de faune secourent, réhabilitent, réintroduisent, et fournissent des soins pour toute la vie aux animaux orphelins et blessés. Comprendre les dynamiques de la population d’un sanctuaire—les motifs d’arrivée, mortalité, et de changements projetés de la taille de la population—permet une planification prudente pour les nécessités du futur. En se basant sur le travail déjà fait sur les dynamiques de la population chimpanzé (Pan troglodytes) dans les sanctuaires du Pan African Sanctuary Alliance (PASA; Faust et al. 2011), nous étendons notre analyse au seul sanctuaire bonobo par PASA. Nous avons analysé les motifs démographiques historiques et avons projeté les futures dynamiques de la population en utilisant un modèle démographique basé sur l’individu. La population augmente de 6.7 per cent par an, poussée par l’arrivée de nouveaux individus (moyenne = 5.5 arrivées par an). Plusieurs scénarios modèles montrent une trajectoire de potentielle croissance pour le sanctuaire. Cette recherche illustre comment modeler les données sur les dynamiques historiques pour informer la capacité future du sanctuaire et les besoins gestionnaires.

Reproduction

2017 ◽  
Author(s):  
Derek Burton ◽  
Margaret Burton
Keyword(s):  
Reproductive Behaviour ◽  
Life Cycles ◽  
Freshwater Species ◽  
Adult Fish ◽  
Reproductive Patterns ◽  
Cell Divisions ◽  
Early Stages ◽  
External Cues ◽  
Neural Factors

Interspecific fish reproductive patterns, outputs and life cycles display the greatest variability within the vertebrates. Early stages of oogenesis can be repeated in adult fish, contrasting with mammals; the pre-set sequence of cell divisions in gametogenesis is otherwise similar and is described in detail. Most fish deposit much yolk (vitellogenesis) in developing eggs. Migrations, beach-spawning and mouth-brooding are some of the interesting variations. Fertilization is predominantly external but is internal in some groups such as chondrichthyans. The omission of annual reproduction is well established in some freshwater species and the idea that this may also be the case for marine teleosts is gaining acceptance. This should be taken into account for intensively fished species. The possible roles of external cues, hormones, pheromones and neural factors acting as ‘switches’ and coordinators in gametogenesis and reproductive behaviour are discussed.

scholarly journals Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

2020 ◽  
Vol 13 (10) ◽  
pp. 2821-2835
Author(s):  
Lei Chen ◽  
Jing‐Tao Sun ◽  
Peng‐Yu Jin ◽  
Ary A. Hoffmann ◽  
Xiao‐Li Bing ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genomic Data ◽  
Spider Mites ◽  
Range Shifts ◽  
Population Genomic

scholarly journals Have Niche, Will Travel. New Means of Linking Diet and Ecomorphology Reveals Niche Conservatism in Freshwater Cottoid Fishes

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
T J Buser ◽  
D L Finnegan ◽  
A P Summers ◽  
M A Kolmann
Keyword(s):  
Niche Conservatism ◽  
Freshwater Species ◽  
Evolutionary Transitions ◽  
Adaptive Diversification ◽  
Functional Aspects ◽  
Ecological Evolution ◽  
Jaw Apparatus ◽  
Cottoid Fishes ◽  
Freshwater Habitats ◽  
Dietary Niche

Synopsis Evolutionary transitions between habitats have been catalysts for some of the most stunning examples of adaptive diversification, with novel niches and new resources providing ecological opportunity for such radiations. In aquatic animals, transitions from saltwater to freshwater habitats are rare, but occur often enough that in the Neotropics for example, marine-derived fishes contribute noticeably to regional ichthyofaunal diversity. Here, we investigate how morphology has evolved in a group of temperate fishes that contain a marine to freshwater transition: the sculpins (Percomorpha; Cottoidea). We devised a novel method for classifying dietary niche and relating functional aspects of prey to their predators. Coupled with functional measurements of the jaw apparatus in cottoids, we explored whether freshwater sculpins have fundamentally changed their niche after invading freshwater (niche lability) or if they retain a niche similar to their marine cousins (niche conservatism). Freshwater sculpins exhibit both phylogeographical and ecological signals of phylogenetic niche conservatism, meaning that regardless of habitat, sculpins fill similar niche roles in either saltwater or freshwater. Rather than competition guiding niche conservatism in freshwater cottoids, we argue that strong intrinsic constraints on morphological and ecological evolution are at play, contra to other studies of diversification in marine-derived freshwater fishes. However, several intertidal and subtidal sculpins as well as several pelagic freshwater species from Lake Baikal show remarkable departures from the typical sculpin bauplan. Our method of prey categorization provides an explicit, quantitative means of classifying dietary niche for macroevolutionary studies, rather than relying on somewhat arbitrary means used in previous literature.

scholarly journals Continental vs. Global Niche-Based Modelling of Freshwater Species’ Distributions: How Big Are the Differences in the Estimated Climate Change Effects?

Water ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 816
Author(s):  
Danijela Markovic ◽  
Jörg Freyhof ◽  
Oskar Kärcher
Keyword(s):  
Climate Change ◽  
Thermal Properties ◽  
Safety Margin ◽  
Thermal Response ◽  
Future Climate Change ◽  
Freshwater Species ◽  
Response Curves ◽  
Preferred Temperature ◽  
Continental Scale ◽  
Management Actions

Thermal response curves that depict the probability of occurrence along a thermal gradient are used to derive various species’ thermal properties and abilities to cope with warming. However, different thermal responses can be expected for different portions of a species range. We focus on differences in thermal response curves (TRCs) and thermal niche requirements for four freshwater fishes (Coregonus sardinella, Pungitius pungitius, Rutilus rutilus, Salvelinus alpinus) native to Europe at (1) the global and (2) European continental scale. European ranges captured only a portion of the global thermal range with major differences in the minimum (Tmin), maximum (Tmax) and average temperature (Tav) of the respective distributions. Further investigations of the model-derived preferred temperature (Tpref), warming tolerance (WT = Tmax − Tpref), safety margin (SM = Tpref − Tav) and the future climatic impact showed substantially differing results. All considered thermal properties either were under- or overestimated at the European level. Our results highlight that, although continental analyses have an impressive spatial extent, they might deliver misleading estimates of species thermal niches and future climate change impacts, if they do not cover the full species ranges. Studies and management actions should therefore favor whole global range distribution data for analyzing species responses to environmental gradients.

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