Periodic Reporting for period 1 - CHROMREP (An integrative approach linking chromosomal evolution and biodiversity in reptiles from Madagascar)
Reporting period: 2018-10-01 to 2020-09-30
Chromosomal evolution is a major, yet under-explored, driver of biodiversity. Changes in chromosome number and morphology influence the generation of new biological diversity, via polyploidization and the accumulation of different chromosome rearrangements. Karyological evolution may also drive the generation of different genetic sex determination systems, via the gain or loss of heterogametic sex chromosomes. These changes can reduce or eliminate recombination with conspecifics and thus generate potential for assortative mating and ultimately speciation and reproductive compatibility in sexually reproducing organisms.
Despite these factors, there are few studies that directly test for the impact of chromosome evolution on phylogenetic and biogeographic diversification in animals.
To better understand processes and mechanisms of chromosomal evolutionary dynamics and to test for the influence of chromosome evolution on animal biodiversity, phylogeny and biogeography CHROMREP employs a multidisciplinary and comparative approach by examining an integrative dataset generated from multiple lineages of reptiles from Madagascar, a unique model region to study biological diversity.
Despite these factors, there are few studies that directly test for the impact of chromosome evolution on phylogenetic and biogeographic diversification in animals.
To better understand processes and mechanisms of chromosomal evolutionary dynamics and to test for the influence of chromosome evolution on animal biodiversity, phylogeny and biogeography CHROMREP employs a multidisciplinary and comparative approach by examining an integrative dataset generated from multiple lineages of reptiles from Madagascar, a unique model region to study biological diversity.
The project’s Research Objectives (RO1-3) and their relative main scientific results were implemented and achieved during the realization of CHROMREP as described as follows:
- RO1 - to evaluate chromosomal evolution of Malagasy reptiles: this objective was achieves using a combination of cytogenetic, molecular and computational methods. More than 70 karyotypes of endemic species of Malagasy reptiles have been described and analysed using different cytogenetic techniques: Giemsa’s staining and fluorochromes, Ag-NOR banding, C-banding and molecular cytogenetics (e.g. Fluorescence in Situ Hybridization of telomeric repeats). The results obtained represent the first chromosomal data of most considered taxa and a novel comprehensive assessment of their karyotype diversity.
A comparative testing of alternative karyotype evolutionary scenarios was performed using phylogenetic comparative methods in the R environment, documenting the occurrence of different chromosome evolutionary trends in different lineages and provided new insights on the diversification of heteromorphic sex chromosome systems.
The original cytogenetic results obtained during the realization of RO1 were further evaluated in the phylogenetic and biogeographic framework obtained during RO2-3.
- RO2 - to assess phylogenetic relationships of Malagasy reptiles: this objective was achieved with experimental procedures at the NHM molecular lab and during the subsequent implementation of a wide range of different computational methods, using a combination of different molecular and phylogenetic approaches. An initial DNA barcoding was used to assess the taxonomy and species richness of the focal Malagasy reptile taxa. A molecular sequencing of a selection of nuclear and mitochondrial markers allowed the generation of novel, comprehensive, time-calibrated phylogenetic assessments of the focal Malagasy reptiles. The phylogenetic inferences obtained at RO2 were used in the evolutionary analysis of chromosomal data obtained at RO1.
- RO3 - to link biogeographic patterns with chromosomal variation in Malagasy reptiles: the combination of the original scientific results obtained at RO1-2, were further analysed using different computational methods. Using the new time-calibrated phylogenies gained from RO2 along with spatial data (from available samples, museum records, the Global Biodiversity Information Facility and literature) CHROMREP characterized the historical biogeography of the different study taxa by testing: (a) ancestral distribution ranges and radiation centres; (b) biogeographic routes of lineage diversification in and out of Madagascar and between different Malagasy ecoregions and (c) the occurrence and significance of processes of dispersal and vicariance.
The dissemination of the project scientific results has been and will be achieved with publications on international, Open Access scientific journals, partecipation to international conferences, invited meetings and seminars and communications on different institutional and scientific website and social media (e.g. the NHM website and online portal, ResearchGate, Twitter).
- RO1 - to evaluate chromosomal evolution of Malagasy reptiles: this objective was achieves using a combination of cytogenetic, molecular and computational methods. More than 70 karyotypes of endemic species of Malagasy reptiles have been described and analysed using different cytogenetic techniques: Giemsa’s staining and fluorochromes, Ag-NOR banding, C-banding and molecular cytogenetics (e.g. Fluorescence in Situ Hybridization of telomeric repeats). The results obtained represent the first chromosomal data of most considered taxa and a novel comprehensive assessment of their karyotype diversity.
A comparative testing of alternative karyotype evolutionary scenarios was performed using phylogenetic comparative methods in the R environment, documenting the occurrence of different chromosome evolutionary trends in different lineages and provided new insights on the diversification of heteromorphic sex chromosome systems.
The original cytogenetic results obtained during the realization of RO1 were further evaluated in the phylogenetic and biogeographic framework obtained during RO2-3.
- RO2 - to assess phylogenetic relationships of Malagasy reptiles: this objective was achieved with experimental procedures at the NHM molecular lab and during the subsequent implementation of a wide range of different computational methods, using a combination of different molecular and phylogenetic approaches. An initial DNA barcoding was used to assess the taxonomy and species richness of the focal Malagasy reptile taxa. A molecular sequencing of a selection of nuclear and mitochondrial markers allowed the generation of novel, comprehensive, time-calibrated phylogenetic assessments of the focal Malagasy reptiles. The phylogenetic inferences obtained at RO2 were used in the evolutionary analysis of chromosomal data obtained at RO1.
- RO3 - to link biogeographic patterns with chromosomal variation in Malagasy reptiles: the combination of the original scientific results obtained at RO1-2, were further analysed using different computational methods. Using the new time-calibrated phylogenies gained from RO2 along with spatial data (from available samples, museum records, the Global Biodiversity Information Facility and literature) CHROMREP characterized the historical biogeography of the different study taxa by testing: (a) ancestral distribution ranges and radiation centres; (b) biogeographic routes of lineage diversification in and out of Madagascar and between different Malagasy ecoregions and (c) the occurrence and significance of processes of dispersal and vicariance.
The dissemination of the project scientific results has been and will be achieved with publications on international, Open Access scientific journals, partecipation to international conferences, invited meetings and seminars and communications on different institutional and scientific website and social media (e.g. the NHM website and online portal, ResearchGate, Twitter).
CHROMOREP reconstructed more than 70 karyotypes of endemic Malagasy species, providing the first chromosomal data of most considered study animals and a novel comprehensive assessment of their karyotype diversity.
The project provided new original insights on different chromosome evolutionary dynamics, identifying the occurrence of distinct evolutionary trends in different lineages, as the conservation and variability of chromosome number and morphology in phylogenies and the diversification of sex chromosome systems. The combination of modern molecular and phylogenetic methods, cytogenetic techniques and computational inferences allowed the identification of the several undescribed species in different evolutionary lineages of the focal reptile taxa, provided a new time-calibrated assessment of their evolutionary relationships and novel insights on their chromosomal evolutionary dynamics and on the endemic Malagasy reptile diversity.
The project provided new original insights on different chromosome evolutionary dynamics, identifying the occurrence of distinct evolutionary trends in different lineages, as the conservation and variability of chromosome number and morphology in phylogenies and the diversification of sex chromosome systems. The combination of modern molecular and phylogenetic methods, cytogenetic techniques and computational inferences allowed the identification of the several undescribed species in different evolutionary lineages of the focal reptile taxa, provided a new time-calibrated assessment of their evolutionary relationships and novel insights on their chromosomal evolutionary dynamics and on the endemic Malagasy reptile diversity.