Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland

Garg, Kritika M.; Chattopadhyay, Balaji; Cros, Emilie; Tomassi, Suzanne; Benedick, Suzan; Edwards, David P.

doi:10.1093/molbev/msab340

Cited by 11 publications

(4 citation statements)

References 75 publications

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“…As studies incorporating hDNA become increasingly common (Colella et al, 2020;Toussaint et al, 2021c;Garg et al, 2022), researchers will be faced with decisions regarding sample selection. Should an ethanol-preserved specimen always be extracted if a museum specimen is available?…”

Section: Sample Preservation and Sequence Capture Successmentioning

confidence: 99%

Predictors of sequence capture in a large-scale anchored phylogenomics project

et al. 2022

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Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.

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Section: Sample Preservation and Sequence Capture Successmentioning

confidence: 99%

Predictors of sequence capture in a large-scale anchored phylogenomics project

et al. 2022

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“…On the other hand, many islands separated by deep‐sea channels have never been physically connected to the continent, yet may host dispersal‐limited species, suggesting a role for overseas dispersal (Cowie & Holland, 2006; Salvi et al, 2021). Therefore, the genetic composition of island populations has been shaped by island‐specific features and species traits, such as spatial isolation, time‐since‐isolation and dispersal capacity (Garg et al, 2022; Heaney et al, 2005; Roberts, 2006; Wang et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Reconstructing the complex colonisation histories of lizards across Mediterranean archipelagos

Sherpa,

Salvi,

Silva‐Rocha

et al. 2023

Journal of Biogeography

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AimThe Mediterranean Basin is a global biodiversity hotspot and has one of the longest histories of human–biota interactions. Islands host a large fraction of Mediterranean diversity and endemism, but the relative importance of natural versus human‐mediated colonisation processes in shaping the distribution and genetic structure of Mediterranean island fauna remains poorly understood. Here, we combine population genomics, demographic models and palaeoshoreline reconstructions to establish the island‐colonisation dynamics of wall lizards in Mediterranean archipelagos.LocationFour Mediterranean archipelagos in Italy and Croatia.TaxonThe wall lizard Podarcis siculus.MethodsWe used ddRAD sequencing to genotype 140 lizards from 23 island and mainland populations. Analyses of admixture and site frequency spectra were used to reconstruct population structure, demographic history and variation of gene flow through time. Genomic results were integrated with palaeogeographical reconstructions and were compared to archaeological evidence of human presence on these islands.ResultsAlthough many island populations of this species are assumed to be non‐native, we find that many islands were colonised long before any known human settlements (230,000–12,000 years ago). This natural colonisation most likely occurred through land bridges during glacial marine regression or by over‐sea rafting. On the other hand, islands distant from the continent were often colonised recently, and some of the estimated island colonisation times match historical records of human arrival. We also determine that long‐established island populations generally show lower genetic diversity compared to proximate mainland populations, contrary to recently colonised islands that must have experienced higher rates of post‐colonisation gene flow.Main ConclusionOur integrated approach provides us with the power to accurately quantify the origin, timing and mode of island colonisation. This framework helps to clarify the biogeographical and evolutionary history of island populations, with important implications for conservation and management of island biodiversity.

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“…The inclusion of degraded samples from natural history collections has been useful for determining the phylogenetic placement (Delling et al, 2023) and biogeography (Garg et al, 2022) of poorly known or extinct lineages. In this study, we phylogenetically place five genera and six species for the first time, each of which are known from only a few voucher specimens, and use these results to formulate hypotheses regarding homalopsid evolution.…”

Section: Museum Genomics Of Homalopsidaementioning

confidence: 99%

“…The sea-level fluctuations of this region are often cited as a driver of speciation and population structure in invertebrates and vertebrates (Li & Li, 2018;Wu et al, 2022;Wüster et al, 2005). However, recent geological studies that better identify the dates of land bridges (Husson et al, 2020;Sarr et al, 2019) suggest that current hypotheses must be revisited to test if newly identified processes in other taxa also affect diversification and dispersal scenarios (Garg et al, 2022;Sholihah et al, 2021).…”

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confidence: 99%

Phylogenomics of Fresh and Formalin Specimens Resolves the Systematics of Old World Mud Snakes (Serpentes: Homalopsidae) and Expands Biogeographic Inference

Bernstein,

De Souza,

Murphy

et al. 2023

BSSB

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Our knowledge of the biodiversity of Asia and Australasia continues to expand with more focused studies on systematics of various groups and their biogeography. Historically, fluctuating sea levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanisms. However, recent research has shown that geological shifts of the mainland and species dispersal events may be better explanations of the biodiversity in these regions. We investigate these processes using the poorly studied and geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a target capture approach of ~4,800 nuclear loci from fresh tissues and supplemental mitochondrial data from formalin tissues from museum specimens. We use these datasets to reconstruct the first resolved phylogeny of the group, identify their biogeographic origins, and test hypotheses regarding the roles of sea-level change and habitat selection on their diversification. Divergence dating and ancestral range estimation yielded support for an Oligocene origin and diversification from mainland Southeast Asia and Sundaland in the rear-fanged group ~20 million years ago, followed by eastward and westward dispersal. GeoHiSSE models indicate that niche expansion of ancestral, rear-fanged lineages into aquatic environments did not impact their diversification rates. Our results highlight that Pleistocene sea-level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae and that, alternatively, geological shifts in mainland Southeast Asia may have been a major driver of diversity in this group. We also emphasize the importance of using fresh and degraded tissues, and both nuclear and mitochondrial DNA, for filling knowledge gaps in poorly known but highly diverse and conceptually important groups. Here, Homalopsidae represents a non-traditional but effective model study system for understanding transitions between terrestrial, marine, and freshwater environments.

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Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland

Cited by 11 publications

References 75 publications

Predictors of sequence capture in a large-scale anchored phylogenomics project

Predictors of sequence capture in a large-scale anchored phylogenomics project

Reconstructing the complex colonisation histories of lizards across Mediterranean archipelagos

Phylogenomics of Fresh and Formalin Specimens Resolves the Systematics of Old World Mud Snakes (Serpentes: Homalopsidae) and Expands Biogeographic Inference

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